13-32380043-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM5PP3_StrongPP5_Very_Strong

The NM_000059.4(BRCA2):​c.9154C>T​(p.Arg3052Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3052Q) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

BRCA2
NM_000059.4 missense

Scores

8
5
3

Clinical Significance

Pathogenic reviewed by expert panel P:35U:1

Conservation

PhyloP100: 2.98
Variant links:
Genes affected
BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PM5
Other missense variant is known to change same aminoacid residue: Variant chr13-32380044-G-A is described in Lovd as [Pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.978
PP5
Variant 13-32380043-C-T is Pathogenic according to our data. Variant chr13-32380043-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 52763.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32380043-C-T is described in Lovd as [Pathogenic]. Variant chr13-32380043-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BRCA2NM_000059.4 linkc.9154C>T p.Arg3052Trp missense_variant Exon 24 of 27 ENST00000380152.8 NP_000050.3 P51587

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BRCA2ENST00000380152.8 linkc.9154C>T p.Arg3052Trp missense_variant Exon 24 of 27 5 NM_000059.4 ENSP00000369497.3 P51587
BRCA2ENST00000530893.7 linkc.8785C>T p.Arg2929Trp missense_variant Exon 24 of 27 1 ENSP00000499438.2 A0A590UJI7
BRCA2ENST00000614259.2 linkn.*1212C>T non_coding_transcript_exon_variant Exon 23 of 26 2 ENSP00000506251.1 A0A7P0TAP7
BRCA2ENST00000614259.2 linkn.*1212C>T 3_prime_UTR_variant Exon 23 of 26 2 ENSP00000506251.1 A0A7P0TAP7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000119
AC:
3
AN:
251190
Hom.:
0
AF XY:
0.0000147
AC XY:
2
AN XY:
135794
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000880
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000547
AC:
8
AN:
1461782
Hom.:
0
Cov.:
32
AF XY:
0.00000688
AC XY:
5
AN XY:
727192
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000670
Hom.:
0
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:35Uncertain:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:12Uncertain:1
May 29, 2002
Breast Cancer Information Core (BIC) (BRCA2)
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Aug 10, 2015
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Significance: Pathogenic
Review Status: reviewed by expert panel
Collection Method: curation

IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 1 -

Jul 01, 2015
Department of Medical Genetics, Oslo University Hospital
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 06, 2023
KCCC/NGS Laboratory, Kuwait Cancer Control Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

BRCA2 (p.Arg3052Trp): This sequence change results in a non-conservative amino acid change located in the OB3 domain of the encoded protein sequence. In-silico prediction show pathogenic computational verdict based on 8 pathogenic predictions from BayesDel_addAF, DANN, FATHMM-MKL, M-CAP, MVP, MutationTaster, REVEL and SIFT vs 2 benign predictions from EIGEN and PrimateAI. It has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer Syndrome (PMID: 20513136 and 23108138). Functional analyses of this variant are published (PMID: 18451181, 23108138, 25146914, 18607349) describing it as deleterious. ClinVar has an entry for this variant (ClinVar 52763) with 25 submissions, all described it as pathogenic, 3 stars, no conflict, and reviewed by an expert panel. Therefore, this variant was classified as pathogenic. -

Apr 10, 2017
Counsyl
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Nov 28, 2012
Sharing Clinical Reports Project (SCRP)
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jan 01, 2017
Genologica Medica
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 02, 2015
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 21, 2015
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 08, 2014
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 27, 2024
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PS3; PP3; PP1; Expert panel -

Mar 02, 2020
BRCAlab, Lund University
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

not provided Pathogenic:8
-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Aug 27, 2023
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Published functional studies demonstrate a damaging effect: impaired homology directed repair activity and cell survival, and increased sensitivity to PARP inhibitors (Farrugia et al., 2008; Kuznetsov et al., 2008; Guidugli et al., 2013; Cunningham et al., 2014; Hendriks et al., 2014; Shimelis et al., 2017; Guidugli et al., 2018; Hart et al., 2019; Ikegami et al., 2020); Observed in individuals with breast or ovarian cancer and reported to segregate with disease in affected family members (Mohammadi et al., 2009; Borg et al., 2010; Capanu et al., 2011; Cunningham et al., 2014; Song et al., 2014; Li et al., 2018); Multifactorial studies suggest this variant is associated with hereditary breast and ovarian cancer (Lindor et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as 9382C>T; This variant is associated with the following publications: (PMID: 18607349, 19043619, 29555025, 28277317, 29176636, 21520273, 25556971, 26221963, 31565484, 30720243, 30078507, 31360874, 20513136, 25782689, 24504028, 24323938, 24728189, 23231788, 21702907, 19200354, 26026974, 20104584, 21120943, 24963051, 19563646, 23108138, 25146914, 18451181, 28199314, 28279176, 28283652, 28487467, 28724667, 25085752, 29339979, 29988080, 29922827, 30728895, 29907814, 26845104, 29446198, 30702160, 29607586, 31159747, 32444794, 34597585, 31980526, 30787465, 35273153, 31907386, 32438681, 29884136, 35264596, 35736817, 33609447, 32853339, 29884841, 31825140, 34399810, 33629534, 35711920, 12228710, 35665744, 21990134, 29394989) -

Oct 01, 2018
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Aug 02, 2021
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The frequency of this variant in the general population, 0.000029 (1/34578 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with breast cancer, ovarian cancer and in healthy controls (PMID: 28724667 (2017), 28283652 (2017), 26845104 (2016), 26221963 (2015), 24728189 (2014), 24504028 (2014), 21520273 (2011), 19563646 (2009), 19200354 (2009)). In addition, functional studies in the published literature demonstrate that this variant is damaging to BRCA2 protein function (PMID: 29394989 (2018), 28283652 (2017), 25146914 (2014), 18607349 (2008), 18451181 (2008)) and has been classified as pathogenic in multifactorial analyses (PMID: 23108138 (2013), 20513136 (2010)). Based on the available information, this variant is classified as pathogenic. -

Jan 25, 2018
Clinical Genetics and Genomics, Karolinska University Hospital
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 14, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The BRCA2 c.9154C>T; p.Arg3052Trp variant (rs45580035) is reported in the medical literature in individuals and families with breast cancer (Farrugia 2008, Lindor 2012, Pruss 2014, Shimelis 2017). The variant is also reported in ClinVar (Variation ID: 52763), but is only observed on three alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The arginine at codon 3052 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.821). Additionally, functional studies demonstrate reduced protein function (Farrugia 2008, Kuznetsov 2008) and odds ratio calculations conclude this variant is pathogenic (Farrugia 2008, Lindor 2012, Pruss 2014, Shimelis 2017). Considering available information, this variant is classified as pathogenic. References: Farrugia DJ et al. Functional assays for classification of BRCA2 variants of uncertain significance. Cancer Res. 2008 May 1;68(9):3523-31. Kuznetsov SG et al. Mouse embryonic stem cell-based functional assay to evaluate mutations in BRCA2. Nat Med. 2008 Aug;14(8):875-81. Lindor NM et al. A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Hum Mutat. 2012 Jan;33(1):8-21. Pruss D et al. Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat. 2014 Aug;147(1):119-32. Shimelis H et al. BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer. Cancer Res. 2017 Jun 1;77(11):2789-2799. -

Feb 12, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PP1_strong, PP3, PP4_moderate, PS3 -

Feb 16, 2024
Clinical Genetics Laboratory, Skane University Hospital Lund
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Hereditary breast ovarian cancer syndrome Pathogenic:6
Apr 19, 2022
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 02, 2018
Mendelics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 15, 2021
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: BRCA2 c.9154C>T (p.Arg3052Trp) results in a non-conservative amino acid change located in the OB3 domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251190 control chromosomes. c.9154C>T has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g. Farrugia_2008, GomezGarcia_2009). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (Farrugia_2008, Kuznetsov_2008, Walker_2010). Ninteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Jan 31, 2014
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Dec 26, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 3052 of the BRCA2 protein (p.Arg3052Trp). This variant is present in population databases (rs45580035, gnomAD 0.003%). This missense change has been observed in individual(s) with breast, ovarian, and prostate cancer (PMID: 18451181, 19200354, 20104584, 24504028, 24728189, 25556971, 26845104). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 52763). Invitae Evidence Modeling incorporating data from in vitro experimental studies (PMID: 33609447) indicates that this missense variant is expected to disrupt BRCA2 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 18451181, 18607349, 23108138, 25146914). For these reasons, this variant has been classified as Pathogenic. -

Apr 20, 2017
Department of Pathology and Molecular Medicine, Queen's University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:3
Nov 10, 2017
True Health Diagnostics
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Feb 02, 2023
Color Diagnostics, LLC DBA Color Health
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This missense variant replaces arginine with tryptophan at codon 3052 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that the variant protein is defective in homology-directed DNA repair and fails to complement BRCA2-deficient mouse embryonic stem cells (PMID: 18451181, 18607349, 24323938, 29394989, 35711920). This variant has been reported in over 12 individuals affected with breast or ovarian cancer and in 1 unaffected individual (PMID: 18451181, 24728189, 25682074, 26221963, 28724667, 33471991). This variant has been reported in several families affected with hereditary breast and ovarian cancer (PMID: 19200354, 25556971) and has been identified in 22 families among the CIMBA participants (PMID: 29446198). It has been shown that this variant segregates with disease with a likelihood ratio of 3.6 from 10 carrier families (PMID: 18451181). This variant has been identified in 3/251190 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Oct 14, 2024
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.R3052W pathogenic mutation (also known as c.9154C>T), located in coding exon 23 of the BRCA2 gene, results from a C to T substitution at nucleotide position 9154. The arginine at codon 3052 is replaced by tryptophan, an amino acid with dissimilar properties. This mutation has been reported in numerous families and individuals with breast and/or ovarian cancer (G&oacute;mez Garc&iacute;a EB et al. Breast Cancer Res. 2009; 11(1):R8; Cunningham JM, Sci Rep 2014; 4:4026; Song H et al. Hum. Mol. Genet., 2014 Sep;23:4703-9; Sun J et al. Clin. Cancer Res., 2017 Oct;23:6113-6119). This alteration has been classified as pathogenic or likely pathogenic by several studies utilizing the following line(s) of evidence: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and/or functional assay results (Karchin R et al. Cancer Inform, 2008 Apr;6:203-16; Mohammadi L et al. BMC Cancer, 2009 Jun;9:211; Capanu M et al. Genet. Epidemiol., 2011 Jul;35:389-97; Lindor NM et al. Hum Mutat. 2012 Jan; 33(1):8-21). Additionally, several functional studies have found this alteration to be pathogenic (Kuznetsov SG et al. Nat. Med., 2008 Aug;14:875-81; Hendriks G et al. Hum. Mutat., 2014 Nov;35:1382-91; Guidugli L et al. Am. J. Hum. Genet., 2018 Jan; Mesman RLS et al. Genet Med 2019 02;21(2):293-302; Richardson ME at al. Am J Hum Genet 2021 03;108(3):458-468 ). Of note, this alteration is also designated as 9382C>T in published literature. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial cancer of breast Pathogenic:2
Jan 01, 2020
GeneKor MSA
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This is a single base substitution replacing Arginine with Tryptophan at codon 3052 of the BRCA2 protein. The arginine residue is highly conserved and there is a large physicochemical difference between arginine and tryptophan (Grantham Score 101). Algorithms developed to predict the effect of missense changes on protein structure and function suggest that this variant is likely to be damaging to the protein. This variant has been described in the international literature in patients affected with breast cancer (PMID: 18451181, PMID: 19200354 , BMC Cancer. 2009, 9:211; PMID: 21520273, PMID: 24504028). Experimental studies have shown that this missense change results in the loss of DNA repair activity of the encoded protein product in vitro (PMID: 18451181,PMID: 18607349). The mutation database ClinVar contains entries for this variant (Variation ID: 52763). -

Feb 23, 2024
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Breast and/or ovarian cancer Pathogenic:1
Nov 01, 2016
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:1
Nov 20, 2015
University of Washington Department of Laboratory Medicine, University of Washington
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

BRCA2-related cancer predisposition Pathogenic:1
Sep 03, 2024
All of Us Research Program, National Institutes of Health
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This missense variant replaces arginine with tryptophan at codon 3052 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that the variant protein is defective in homology-directed DNA repair and fails to complement BRCA2-deficient mouse embryonic stem cells (PMID: 18451181, 18607349, 24323938, 29394989, 35711920). This variant has been reported in over 12 individuals affected with breast or ovarian cancer and in 1 unaffected individual (PMID: 18451181, 24728189, 25682074, 26221963, 28724667, 33471991). This variant has been reported in several families affected with hereditary breast and ovarian cancer (PMID: 19200354, 25556971) and has been identified in 22 families among the CIMBA participants (PMID: 29446198). It has been shown that this variant segregates with disease with a likelihood ratio of 3.6 from 10 carrier families (PMID: 18451181). This variant has been identified in 3/251190 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Malignant tumor of breast Pathogenic:1
-
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

The BRCA2 p.Arg3052Trp variant was identified in 5 of 10664 proband chromosomes (frequency: 0.0005) from individuals or families with breast and ovarian cancer (Borg 2010, Cunningham 2014, Trujillano 2015, Song 2014). The variant was also identified in the following databases: dbSNP (ID: rs45580035) as "With Pathogenic allele", ClinVar (13x pathogenic, 1x uncertain significance), Clinvitae (6X pathogenic), LOVD 3.0 (reported 50x, predicted deleterious), UMD-LSDB (10 records, causal), BIC Database (8x, clinical importance unknown), and ARUP Laboratories (definitely pathogenic). The variant was not identified in Cosmic, MutDB, or the Zhejiang Colon Cancer Database. The variant was identified in control databases in 3 of 246052 chromosomes at a frequency of 0.00001 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Latino in 1 of 33572 chromosomes (freq: 0.00003), European in 1 of 111550 chromosomes (freq: 0.000009), and South Asian in 1 of 30782 chromosomes (freq: 0.00003). The variant was not observed in the African, Other, Ashkenazi Jewish, East Asian, or Finnish populations. Functional studies investigating the DNA break repair activity of p.Arg3052Trp showed reduced activity of this variant (Farrugia 2008, Guidugli 2013). A study using mouse embryonic stem cells and bacterial artificial chromosomes demonstrated that cells expressing p.Arg3052Trp did not survive, suggesting it to be deleterious (Borg 2010). The p.Arg3052 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.67
BayesDel_addAF
Pathogenic
0.34
D
BayesDel_noAF
Pathogenic
0.35
CADD
Uncertain
24
DANN
Uncertain
1.0
Eigen
Uncertain
0.26
Eigen_PC
Benign
0.16
FATHMM_MKL
Uncertain
0.85
D
M_CAP
Pathogenic
0.48
D
MetaRNN
Pathogenic
0.98
D;D
MetaSVM
Uncertain
0.60
D
PrimateAI
Uncertain
0.51
T
PROVEAN
Benign
-2.1
N;N
REVEL
Pathogenic
0.82
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0
D;D
Vest4
0.76
MutPred
0.92
Gain of catalytic residue at R3052 (P = 0.0416);Gain of catalytic residue at R3052 (P = 0.0416);
MVP
0.96
MPC
0.17
ClinPred
0.95
D
GERP RS
1.4
gMVP
0.86

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs45580035; hg19: chr13-32954180; API