rs61754388

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PM1PP2PP5_Very_Strong

The NM_000372.5(TYR):​c.1118C>A​(p.Thr373Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000882 in 1,613,434 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. T373T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00049 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00092 ( 1 hom. )

Consequence

TYR
NM_000372.5 missense

Scores

6
9
4

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:26O:1

Conservation

PhyloP100: 5.70

Publications

31 publications found
Variant links:
Genes affected
TYR (HGNC:12442): (tyrosinase) The enzyme encoded by this gene catalyzes the first 2 steps, and at least 1 subsequent step, in the conversion of tyrosine to melanin. The enzyme has both tyrosine hydroxylase and dopa oxidase catalytic activities, and requires copper for function. Mutations in this gene result in oculocutaneous albinism, and nonpathologic polymorphisms result in skin pigmentation variation. The human genome contains a pseudogene similar to the 3' half of this gene. [provided by RefSeq, Oct 2008]
TYR Gene-Disease associations (from GenCC):
  • oculocutaneous albinism type 1
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • oculocutaneous albinism type 1A
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
  • Waardenburg syndrome type 2
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • minimal pigment oculocutaneous albinism type 1
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • oculocutaneous albinism type 1B
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • temperature-sensitive oculocutaneous albinism type 1
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 11 ACMG points.

PM1
In a hotspot region, there are 14 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 11 uncertain in NM_000372.5
PP2
Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 116 curated pathogenic missense variants (we use a threshold of 10). The gene has 3 curated benign missense variants. Gene score misZ: -1.9514 (below the threshold of 3.09). Trascript score misZ: -0.85521 (below the threshold of 3.09). GenCC associations: The gene is linked to Waardenburg syndrome type 2, oculocutaneous albinism type 1A, oculocutaneous albinism type 1, oculocutaneous albinism type 1B, minimal pigment oculocutaneous albinism type 1, temperature-sensitive oculocutaneous albinism type 1.
PP5
Variant 11-89227904-C-A is Pathogenic according to our data. Variant chr11-89227904-C-A is described in ClinVar as Pathogenic. ClinVar VariationId is 3774.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TYRNM_000372.5 linkc.1118C>A p.Thr373Lys missense_variant Exon 3 of 5 ENST00000263321.6 NP_000363.1 P14679-1L8B082
TYRXM_011542970.3 linkc.1118C>A p.Thr373Lys missense_variant Exon 3 of 6 XP_011541272.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TYRENST00000263321.6 linkc.1118C>A p.Thr373Lys missense_variant Exon 3 of 5 1 NM_000372.5 ENSP00000263321.4 P14679-1

Frequencies

GnomAD3 genomes
AF:
0.000493
AC:
75
AN:
152014
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
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:
0.000971
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.000343
AC:
86
AN:
250994
AF XY:
0.000413
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.0000580
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000463
Gnomad NFE exome
AF:
0.000687
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000922
AC:
1348
AN:
1461420
Hom.:
1
Cov.:
32
AF XY:
0.000873
AC XY:
635
AN XY:
727014
show subpopulations
African (AFR)
AF:
0.0000897
AC:
3
AN:
33460
American (AMR)
AF:
0.000112
AC:
5
AN:
44662
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26120
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39670
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86254
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53380
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
0.00112
AC:
1246
AN:
1111728
Other (OTH)
AF:
0.00156
AC:
94
AN:
60380
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
69
137
206
274
343
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
52
104
156
208
260
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000493
AC:
75
AN:
152014
Hom.:
0
Cov.:
32
AF XY:
0.000471
AC XY:
35
AN XY:
74248
show subpopulations
African (AFR)
AF:
0.000169
AC:
7
AN:
41392
American (AMR)
AF:
0.000131
AC:
2
AN:
15234
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5180
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10592
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.000971
AC:
66
AN:
68002
Other (OTH)
AF:
0.00
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
4
8
11
15
19
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000749
Hom.:
0
Bravo
AF:
0.000468
TwinsUK
AF:
0.00162
AC:
6
ALSPAC
AF:
0.00156
AC:
6
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000814
AC:
7
ExAC
AF:
0.000313
AC:
38
EpiCase
AF:
0.000819
EpiControl
AF:
0.000356

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:26Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:7Other:1
Mar 27, 2017
Eurofins Ntd Llc (ga)
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

-
Retina International
Significance:not provided
Review Status:no classification provided
Collection Method:literature only

- -

-
Clinical Genetics, Academic Medical Center
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This sequence change replaces threonine, which is neutral and polar, with lysine, which is basic and polar, at codon 373 of the TYR protein (p.Thr373Lys). This variant is present in population databases (rs61754388, gnomAD 0.07%). This missense change has been observed in individuals with oculocutaneous albinism (PMID: 2342539, 9259202, 13680365, 18326704; internal data). It has also been observed to segregate with disease in related individuals. This variant is also known as Thr355Lys. ClinVar contains an entry for this variant (Variation ID: 3774). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TYR protein function. Experimental studies have shown that this missense change affects TYR function (PMID: 1429711, 9242509, 27775880). For these reasons, this variant has been classified as Pathogenic. -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Jun 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

TYR: PM3:Very Strong, PM2, PP4, PS3:Supporting -

Jan 17, 2022
GeneDx
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Published functional studies demonstrate a damaging effect, specifically, T373K transfected cells had no tyrosine hydroxylase activity, undetectable melanin production, and showed the T373K mutant protein was unable to leave the endoplasmic reticulum (Tripathi et al., 1992; Toyofuku et al., 2001). A separate in vitro study also suggests improper folding of the T373K protein (Dolinska et al., 2017); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 9242509, 11284711, 23085273, 2342539, 27775880, 28484254, 1429711, 27535533, 18463683, 29036293, 28555837, 25533962, 31233279, 31719542, 28976636, 32543925, 31980526, 31589614, 33077847) -

Oculocutaneous albinism type 1A Pathogenic:7
Apr 16, 2024
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jun 25, 2015
Genetic Services Laboratory, University of Chicago
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jul 22, 2021
Genome-Nilou Lab
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Nov 05, 2021
Genetics and Molecular Pathology, SA Pathology
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jul 22, 2022
MGZ Medical Genetics Center
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Oct 10, 2022
Johns Hopkins Genomics, Johns Hopkins University
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This TYR variant (rs61754388) is rare (<0.1%) in a large population dataset (gnomAD: 100/282382 total alleles; 0.035%; no homozygotes) and has been reported in ClinVar. It is one of the most commonly reported TYR variants in individuals of European ancestry with OCA1. This variant has been observed in a homozygous or compound heterozygous state with another pathogenic TYR variant and has been shown to segregate with disease in affected families. This amino acid substitution (p.Thr373Lys) disrupts a signal for N-glycosylation, which results in incomplete processing of the tyrosinase enzyme to its mature glycosylated form and retention of the protein in the endoplasmic reticulum (ER). Experimental studies in transfected HeLa cells demonstrate that the p.Thr373Lys variant abolishes catalytic activity. We consider c.1118C>A to be pathogenic. -

Jul 15, 1992
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only

- -

Oculocutaneous albinism Pathogenic:4
Jul 17, 2023
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with oculocutaneous albinism, TYR-related (MONDO:0018910). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from threonine to lysine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (100 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (p.(Thr373Ala): 1 heterozygote, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated tyrosinase domain (NCBI). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple individuals with albinism or ocular albinism (ClinVar, PMIDs: 2342539, 18326704, 29345414). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been identified in a family with at least four affected individuals (PMID: 2342539). (SP) 1205 - This variant has been shown to be maternally inherited (by carrier screening analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The TYR c.1118C>A (p.Thr373Lys) missense variant has been reported in seven studies in which it is found in a total of 35 patients with oculocutaneous albinism, including in one in a homozygous state, in 29 in a compound heterozygous state (including one sibling pair and three sisters), and in five in a heterozygous state. None of the affected individuals demonstrated detectable tyrosinase activity, with carriers having low activity compared to controls (Spritz et al. 1990; Oetting et al. 1991; Tripathi et al. 1992; Park et al. 1993; Oetting et al. 1993; Hutton et al. 2008; Gargiulo et al. 2011). Segregation of the p.Thr373Lys variant with disease was shown in several of the studies (Spritz RA et al. 1990; Park et al. 1993; Gargiulo et al. 2011). The p.Thr373Lys variant was absent from 26 control alleles but is reported at a frequency of 0.00081 in the European American population of the Exome Sequencing Project. The Thr373 residue is conserved and located in the region of the protein involved in binding copper which is necessary for catalytic activity (Tripathi et al. 1992). Park et al. (1993) showed that the variant protein was not processed to the mature glycosylated form. Immunohistochemistry studies in COS7 cells by Toyofuku et al. (2001) showed that the p.Thr373Lys variant protein is retained in the ER, in contrast to the wild type protein. Transient expression studies in transfected HeLa cells demonstrated that the p.Thr373Lys variant abolished all three catalytic activities associated with the wild type tyrosinase and was unable to produce melanin (Tripathi et al. 1992). Based on the collective evidence, the p.Thr373Lys variant is classified as pathogenic for oculocutaneous albinism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Jan 15, 2020
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The Thr373Lys variant in TYR has been reported in >40 individuals with Oculocutaneous albinism and was found to segregate with disease in 3 affected relatives from 1 family (Spritz 1990, Gershoni-Baruch 1994, King 2003, Opitz 2004, Hutton 2008, Hutton 2008, Cargiulo 2011). It has also been identified in 0.07% (88/128890) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org) and has been reported in ClinVar (Variation ID: 3774). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies suggest this variant leads to abolished TYR activity (Tripathi 1992). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Oculocutaneous albinism. ACMG/AMP Criteria applied: PM3_Very Strong, PP1_Strong, PS3_Moderate. -

Aug 08, 2024
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Variant summary: TYR c.1118C>A (p.Thr373Lys) results in a non-conservative amino acid change located in the Tyrosinase copper-binding domain (IPR002227) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00034 in 250994 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in TYR causing Oculocutaneous Albinism (0.00034 vs 0.0056), allowing no conclusion about variant significance. c.1118C>A has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Albinism (e.g. Lasseaux_2018). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 29345414). ClinVar contains an entry for this variant (Variation ID: 3774). Based on the evidence outlined above, the variant was classified as pathogenic. -

Oculocutaneous albinism type 1B Pathogenic:2
Feb 19, 2024
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This sequence variant is a single nucleotide substitution (C>A) at position 1118 of the coding sequence of the TYR gene that results in a threonine to lysine amino acid change at residue 373 of the tyrosinase protein. The 373 residue falls in the tyrosinase domain (UniProt). This is a previously reported variant (ClinVar 3774) and is one of the most common variants associated oculocutaneous albinism in both the homozygous and compound heterozygous states (PMID: 1642278, 13680365, 27734839, 30472657, 15146472, 18326704, 23504663, 13680365). This variant is present in 161 of 403008 alleles (0.0399%) in the gnomAD population dataset. Bioinformatic tools provide conflicting predictions concerning the impact of this variant, and the Thr373 residue at this position is highly conserved across the vertebrate species examined. Functional studies have demonstrated that the protein resulting from this variant has nearly no tyrosinase activity, produces nearly no melanin, fails to leave the endoplasmic reticulum, and is degraded (PMID: 11284711, 1429711, 9242509, 27775880). Based upon the evidence, we consider this variant to be pathogenic. ACMG Criteria: PM3, PP2, PS3, PS4 -

Oct 10, 2022
Johns Hopkins Genomics, Johns Hopkins University
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This TYR variant (rs61754388) is rare (<0.1%) in a large population dataset (gnomAD: 100/282382 total alleles; 0.035%; no homozygotes) and has been reported in ClinVar. It is one of the most commonly reported TYR variants in individuals of European ancestry with OCA1. This variant has been observed in a homozygous or compound heterozygous state with another pathogenic TYR variant and has been shown to segregate with disease in affected families. This amino acid substitution (p.Thr373Lys) disrupts a signal for N-glycosylation, which results in incomplete processing of the tyrosinase enzyme to its mature glycosylated form and retention of the protein in the endoplasmic reticulum (ER). Experimental studies in transfected HeLa cells demonstrate that the p.Thr373Lys variant abolishes catalytic activity. We consider c.1118C>A to be pathogenic. -

TYR-related disorder Pathogenic:2
Jul 28, 2023
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

PS3, PM3_Very Strong, PP3 -

May 02, 2024
PreventionGenetics, part of Exact Sciences
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

The TYR c.1118C>A variant is predicted to result in the amino acid substitution p.Thr373Lys. This variant has been reported as causative for oculocutaneous albinism when present with a second pathogenic variant (Opitz et al. 2004. PubMed ID: 15146472; King et al. 2003. PubMed ID: 13680365; Hutton & Spritz. 2008. PubMed ID: 18463683). This variant is reported in 0.068% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant has been classified as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/3774/). Given all the evidence, we interpret this variant as pathogenic. -

SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN Pathogenic:2
Mar 30, 2024
Baylor Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Genomics England Pilot Project, Genomics England
Significance:Likely pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Oculocutaneous albinism type 1B;C2677190:SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN;C4551504:Oculocutaneous albinism type 1A Pathogenic:1
Mar 06, 2024
Fulgent Genetics, Fulgent Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Oculocutaneous albinism type 1B;C4551504:Oculocutaneous albinism type 1A Pathogenic:1
Sep 22, 2024
Clinical Genomics Laboratory, Washington University in St. Louis
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The TYR c.1118C>A (p.Thr373Lys) variant has been reported in several individuals affected with oculocutaneous albinism in the compound heterozygous state (Gershoni-Baruch R et al., PMID: 8128955; Hutton SM and Spritz RA, PMID: 18326704; King RA et al., PMID: 13680365). This variant has been reported in the ClinVar database as a germline pathogenic variant by several submitters. This variant is only observed on 100/282,382 alleles in the general population (gnomAD v.2.1.1), indicating it is not a common variant. Computational predictors indicate that the variant is damaging, evidence that correlates with impact to TYR function. In support of this prediction, a functional study indicates that the variant protein shows no enzymatic activity (Dolinska MB et al., PMID: 27775880). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.71
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Pathogenic
0.39
CADD
Uncertain
24
DANN
Uncertain
0.97
DEOGEN2
Pathogenic
0.96
D
Eigen
Benign
0.049
Eigen_PC
Benign
0.16
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.83
T
M_CAP
Uncertain
0.25
D
MetaRNN
Uncertain
0.73
D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Uncertain
2.7
M
PhyloP100
5.7
PrimateAI
Uncertain
0.61
T
PROVEAN
Uncertain
-3.8
D
REVEL
Pathogenic
0.71
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.0030
D
Polyphen
0.0010
B
Vest4
0.77
MVP
1.0
MPC
0.011
ClinPred
0.27
T
GERP RS
4.5
Varity_R
0.90
gMVP
0.87
Mutation Taster
=58/42
disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs61754388; hg19: chr11-88961072; API