rs41293463

chr17-43051071-A-Cchr17-43051071-A-Gchr17-43051071-A-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_007294.4(BRCA1):c.5324T>G(p.Met1775Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,936 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. M1775K) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: BRCA1 NM_007294.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:20 U:1 O:1
• Conservation: PhyloP100: 5.03

Genes affected

BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 9 benign, 17 uncertain in NM_007294.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-43051071-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 17695.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.901
• PP5: Variant 17-43051071-A-C is Pathogenic according to our data. Variant chr17-43051071-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 17694.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43051071-A-C is described in Lovd as [Pathogenic]. Variant chr17-43051071-A-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.5324T>G	p.Met1775Arg	missense_variant	20/23	ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.5324T>G	p.Met1775Arg	missense_variant	20/23	1	NM_007294.4	P4

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152144 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000119 AC: 3 AN: 251394 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135902

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461792 Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3 AN XY: 727196

Gnomad4 AFR exome AF: 0.000119

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152144 Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1 AN XY: 74332

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000264

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:20 Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:7 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Aug 10, 2015	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 -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Jul 14, 2015	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 07, 2006	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 06, 2024	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genologica Medica	Jan 01, 2017	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	May 29, 2002	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	May 01, 2012	- -

Hereditary breast ovarian cancer syndrome Pathogenic:5

Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Dec 17, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 20, 2016	Variant summary: The BRCA1 c.5324T>G (p.Met1775Arg) variant involves the alteration of a conserved nucleotide and results in a replacement of a medium size and hydrophobic Methionine (M) with a large size and basic Arginine (R) located in the BRCT domain. Consistently, 5/5 in silico tools predict a damaging outcome for this variant. The variant is absent in 124492 control chromosomes while it was reported in several HBOC patients including one family in which it was shown to co-segregate with the disease, indicating its pathogenicity. Moreover, functional studies demonstrated the variant to impair homology directed repair, single strand annealing, phosphopeptide-binding and transcriptional activity of BRCA1 further supporting a deleterious impact. Additionally, multiple clinical diagnostic laboratories/reputable databases classified this variant as Pathogenic. Taken together, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 09, 2023	The p.Met1775Arg variant in BRCA1 has been reported in >20 individuals with BRCA1-associated cancers, with a higher prevalence in those of African descent and segregated with disease in many affected relatives from a large family (Futreal 1994 PMID: 7939630, Miki 1994 PMID: 7545954, Hall 2009 PMID: 19241424, Fackenthal 2012 PMID: 22034289, Pal 2015 PMID: 26287763, BIC database). It has also been identified in 0.002% (1/41432) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). This frequency is low enough to be consistent with the frequency of hereditary breast and ovarian cancer (HBOC) in the general population. In vitro functional studies support an impact on protein function (Kawai 2002 PMID: 12400015, Caligo 2009 PMID: 18680205, Lee 2010 PMID: 20516115, Findlay 2018 PMID: 30209399) and computational prediction tools and conservation analysis suggest that the p.Met1775Arg variant may impact the protein. Additionally, this variant has been classified in ClinVar as Pathogenic on Aug 10, 2015 by the ClinGen-approved ENIGMA expert panel (Variation ID: 17694). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HBOC. ACMG/AMP Criteria applied: PS4, PP1_Moderate, PM2_Supporting, PS3_Moderate, PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 27, 2023	This sequence change replaces methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 1775 of the BRCA1 protein (p.Met1775Arg). This variant is present in population databases (rs41293463, gnomAD 0.02%). This missense change has been observed in individual(s) with breast cancer (PMID: 7545954, 7939630, 22144684). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 17694). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 30209399) indicates that this missense variant is expected to disrupt BRCA1 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects BRCA1 function (PMID: 12400015, 14534301, 19493677, 20516115, 23161852). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	research	Hereditary Cancer Genetics group, Vall d'Hebron Institute of Oncology	Mar 01, 2019	- -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 20, 2021	The BRCA1 c.5324T>G; p.Met1775Arg variant (rs41293463), also known as 5443T>G for traditional nomenclature, is reported in the literature in several individuals and families with hereditary breast and ovarian cancer syndrome (Carter 2018, Futreal 1994, Miki 1994), and shown to co-segregate with disease in at least one family (Miki 1994). Functional analyses of the variant protein show reduced protein stability and a severe impact on BRCA1 function (Caligo 2009, Fernandes 2019, Lee 2010, Towler 2013, Williams 2003). This variant is classified as pathogenic by an expert review panel in ClinVar (Variation ID: 17694). This variant is found in the general population with an overall allele frequency of 0.001% (4/282786 alleles) in the Genome Aggregation Database. The methionine at codon 1775 is located in the highly conserved BRCT repeat domain of BRCA1, and computational analyses predict that this variant is deleterious (REVEL: 0.728). Based on available information, this variant is considered to be pathogenic. References: Caligo MA et al. A yeast recombination assay to characterize human BRCA1 missense variants of unknown pathological significance. Hum Mutat. 2009 Jan;30(1):123-33. Carter NJ et al. Germline pathogenic variants identified in women with ovarian tumors. Gynecol Oncol. 2018 Dec;151(3):481-488. Fernandes VC et al. Impact of amino acid substitutions at secondary structures in the BRCT domains of the tumor suppressor BRCA1: Implications for clinical annotation. J Biol Chem. 2019 Apr 12;294(15):5980-5992. Futreal PA et al. BRCA1 mutations in primary breast and ovarian carcinomas. Science. 1994 Oct 7;266(5182):120-2. Lee MS et al. Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Res. 2010 Jun 15;70(12):4880-90. Miki Y et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994 Oct 7;266(5182):66-71. Towler WI et al. Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing. Hum Mutat. 2013 Mar;34(3):439-45. Williams RS et al. Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. J Biol Chem. 2003 Dec 26;278(52):53007-16. -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The p.Met1775Arg variant was identified in the UMD 2X as a causal variant, in BIC 31X as a variant of unknown clinical importance, and also in the HGMD and LOVD databases. The variant was identified in dbSNP (ID#rs41293463) as a clinically associated SNP, with no population frequency data. In addition, this variant was not identified in 1000 control chromosomes from healthy individuals from one study (Phelan 2005), and was not reported in the Exome Variant Server ESP Project. This variant has been found to segregate with disease in one kindred (Miki 1994). The p.Met1775 residue is conserved across mammals and computational analyses (PolyPhen2, SIFT, AlignGVGD, BLOSUM) suggest that the p.Met1775Arg variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. Several functional studies have concluded that this variant has a deleterious effect on BRCA1 protein function. The mutation has been shown to inhibit the interaction of BRCA1 with the DNA helicase BACH1 (Clapperton 2004, Shiozaki 2004) and with the transcriptional corepressor CtIP (Varma 2005), and yeast and mammalian cell-based assays have demonstrated that the variant impairs transcription activation (Monteiro 1996, Phelan 2005, Tischkowitz 2008). One study utilized a proteolytic sensitivity assay which indicated that the variant results in a folding defect in the BRCT domains, and thus destabilization of this domain (Williams 2003). The authors of this study suggest that this abrogates BRCA1 function, and may explain the spectrum of defects observed in other studies. In summary, based on the above information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 20, 2022	Multifactorial studies suggest this variant is associated with hereditary breast and ovarian cancer (Lindor 2012); Published functional studies demonstrate a damaging effect: abolishes BRCA1 activity, including double strand break repair, transcription, and binding functions (Monteiro 1996, Kawai 2002, Williams 2003, Varma 2005, Towler 2013); Observed in many individuals with hereditary breast and ovarian cancer and has been reported as a recurrent variant in the African population (Futreal 1994, Miki 1994, Zhang 2012, Donenberg 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 5443T>G; This variant is associated with the following publications: (PMID: 21666281, 19493677, 25782689, 17305420, 17308087, 16101277, 15133503, 15967981, 22739995, 26287763, 27495310, 23994874, 22646717, 21447777, 21520273, 8872468, 21922593, 18680205, 15235020, 7939630, 23161852, 12400015, 12427738, 16452482, 8942979, 20516115, 20737206, 11301010, 15133502, 17005433, 17063491, 1749388, 15689452, 16786532, 14729053, 20378548, 27469594, 7545954, 16528612, 27272900, 26681312, 28398198, 25085752, 29337092, 29106372, 28781887, 30209399, 29446198, 31343793, 33087888, 33087929, 30322717, 30765603, 31998812, 30787465, 33646313, 21990134) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 27, 2019	This variant has been reported in individuals and families affected with breast or ovarian cancer in the published literature (PMID: 7939630 (1994) and 7545954 (1994)). It has also been reported to be damaging to BRCA1 protein function (PMID: 23161852 (2013), 20516115 (2010), 19493677 (2009), 14534301 (2003), 12400015 (2002)). Based on the available information, this variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 25, 2021	The p.M1775R pathogenic mutation (also known as c.5324T>G), located in coding exon 19 of the BRCA1 gene, results from a T to G substitution at nucleotide position 5324. The methionine at codon 1775 is replaced by arginine, an amino acid with similar properties. One functional study found that this nucleotide substitution is deleterious in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature. 2018 10;562(7726):217-222). Numerous other functional studies have also found this variant to be deleterious (Easton DF et al. Am. J. Hum. Genet. 2007 Nov;81:873-83; Lee MS et al. Cancer Res. 2010 Jun;70:4880-90; Lindor NM et al. Hum. Mutat. 2012 Jan;33:8-21; Vallee M et al. Hum. Mutat. 2012 Jan;33:22-8; Towler WI et al. Hum Mutat. 2013 Mar;34:439-45; Petitalot A et al. Mol Cancer Res. 2019 01;17:54-69). The p.M1775R alteration was also identified in a large, worldwide study of BRCA1/2 mutation-positive families (Rebbeck TR et al. Hum Mutat. 2018 05;39:593-620). This alteration is located in the highly conserved BRCT repeat domain of BRCA1 and has been shown to have a severe impact on normal BRCA1 function/activity (Carvalho M et al. Cancer Res. 2007 Feb;67:1494-501; Nikolopoulos G et al. Biochim. Biophys. Acta. 2007 Jun;1774:772-80). Of note, this alteration is also designated as 5443T>G in some published literature. Based on the available evidence, this alteration is classified as a pathogenic mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 04, 2024	This missense variant replaces methionine with arginine at codon 1775 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have shown that this variant impacts BRCA1 function in homology-directed DNA repair, transcription activation, haploid cell proliferation and protease sensitivity and protein-protein binding assays (PMID: 8942979, 9738006, 11301010, 12427738, 15689452, 23161852, 30209399). This variant has been reported as a recurring mutation and detected in multiple individuals affected with breast and/or ovarian cancer (PMID: 7837387, 7939630, 18284688, 19491284, 20104584, 24240112, 26287763, 27469594, 29337092, 34204722). This variant also has been reported to segregate with disease in a large pedigree with 24 cases of breast and ovarian cancer (PMID: 7545954). This variant has been identified in 4/282786 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Nov 06, 2017

- -

BRCA1-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Mar 28, 2024

PS3, PS4, PP1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Pathogenic	0.39
CADD	Uncertain	24
DANN	Uncertain	0.99
Eigen	Pathogenic	0.70
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.96	D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.80	D
MetaRNN	Pathogenic	0.90	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.69	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-4.3	D;N;.;D;.;.;N;D
REVEL	Pathogenic	0.73
Sift	Uncertain	0.0030	D;D;.;D;.;.;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D
Polyphen		1.0, 1.0	.;D;.;.;.;D;.;.
Vest4		0.98
MVP		0.96
MPC		0.55
ClinPred		0.94	D
GERP RS		5.2
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.7
Varity_R		0.95
gMVP		0.87

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

Other links and lift over

dbSNP: rs41293463; hg19: chr17-41203088;