rs137852339

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 11P and 2B. PM1PP2PP5_Very_StrongBP4BS2_Supporting

The NM_001360016.2(G6PD):​c.949G>A​(p.Glu317Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,211,171 control chromosomes in the GnomAD database, including 7 homozygotes. There are 376 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.00026 ( 0 hom., 20 hem., cov: 24)
Exomes 𝑓: 0.00059 ( 7 hom. 356 hem. )

Consequence

G6PD
NM_001360016.2 missense

Scores

4
6
5

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:21O:3

Conservation

PhyloP100: 2.83

Publications

29 publications found
Variant links:
Genes affected
G6PD (HGNC:4057): (glucose-6-phosphate dehydrogenase) This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
G6PD Gene-Disease associations (from GenCC):
  • anemia, nonspherocytic hemolytic, due to G6PD deficiency
    Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • G6PD deficiency
    Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
  • class I glucose-6-phosphate dehydrogenase deficiency
    Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

PM1
In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in NM_001360016.2
PP2
Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 185 curated pathogenic missense variants (we use a threshold of 10). The gene has 42 curated benign missense variants. Gene score misZ: 2.0008 (below the threshold of 3.09). Trascript score misZ: NaN (below the threshold of 3.09). GenCC associations: The gene is linked to anemia, nonspherocytic hemolytic, due to G6PD deficiency, class I glucose-6-phosphate dehydrogenase deficiency, G6PD deficiency.
PP5
Variant X-154533044-C-T is Pathogenic according to our data. Variant chrX-154533044-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 10401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP4
Computational evidence support a benign effect (MetaRNN=0.013208687). . Strength limited to SUPPORTING due to the PP5.
BS2
High Hemizygotes in GnomAd4 at 20 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001360016.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
G6PD
NM_001360016.2
MANE Select
c.949G>Ap.Glu317Lys
missense
Exon 9 of 13NP_001346945.1
G6PD
NM_000402.4
c.1039G>Ap.Glu347Lys
missense
Exon 9 of 13NP_000393.4
G6PD
NM_001042351.3
c.949G>Ap.Glu317Lys
missense
Exon 9 of 13NP_001035810.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
G6PD
ENST00000393562.10
TSL:1 MANE Select
c.949G>Ap.Glu317Lys
missense
Exon 9 of 13ENSP00000377192.3
G6PD
ENST00000696421.1
c.949G>Ap.Glu317Lys
missense
Exon 9 of 13ENSP00000512616.1
G6PD
ENST00000369620.6
TSL:5
c.1087G>Ap.Glu363Lys
missense
Exon 9 of 13ENSP00000358633.2

Frequencies

GnomAD3 genomes
AF:
0.000257
AC:
29
AN:
113000
Hom.:
0
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00909
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000751
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.00124
AC:
227
AN:
183230
AF XY:
0.00195
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000612
Gnomad OTH exome
AF:
0.00110
GnomAD4 exome
AF:
0.000595
AC:
653
AN:
1098117
Hom.:
7
Cov.:
33
AF XY:
0.000979
AC XY:
356
AN XY:
363511
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
26400
American (AMR)
AF:
0.00
AC:
0
AN:
35205
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19386
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30205
South Asian (SAS)
AF:
0.0111
AC:
601
AN:
54147
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40451
Middle Eastern (MID)
AF:
0.00145
AC:
6
AN:
4136
European-Non Finnish (NFE)
AF:
0.0000119
AC:
10
AN:
842091
Other (OTH)
AF:
0.000781
AC:
36
AN:
46096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
27
55
82
110
137
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<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:
0.000257
AC:
29
AN:
113054
Hom.:
0
Cov.:
24
AF XY:
0.000568
AC XY:
20
AN XY:
35206
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
31209
American (AMR)
AF:
0.00
AC:
0
AN:
10835
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2652
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3564
South Asian (SAS)
AF:
0.00911
AC:
25
AN:
2744
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6357
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
219
European-Non Finnish (NFE)
AF:
0.0000751
AC:
4
AN:
53259
Other (OTH)
AF:
0.00
AC:
0
AN:
1533
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.569
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
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:
0.000134
Hom.:
1
Bravo
AF:
0.0000982
ExAC
AF:
0.00166
AC:
202

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:21Other:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:12
Apr 01, 2023
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)
Significance:Likely pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

Apr 04, 2024
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Aug 12, 2022
Dunham Lab, University of Washington
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:curation

Variant found in unrelated hemizygotes with G6PD deficiency but no other symptoms (PS4_M, PP4). Also segregates with deficiency in multiple brothers, and heterozygous sister has slightly decreased activity (PP1). Decreased activity in red blood cells of hemizygotes (19-52%) (PS3). Modeling predicts disruption of function (PP3). Reported as pathogenic by multiple clinical testing groups (PP5). Post_P 0.994 (odds of pathogenicity 1517, Prior_P 0.1).

Jun 22, 2023
Neuberg Centre For Genomic Medicine, NCGM
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The observed missense variant c.949G>A (p.Glu317Lys) in G6PD gene has been reported previously in multiple individuals affected with Glucose-6-phosphate dehydrogenase (G6PD) deficiency (Sarker SK, et al., 2016, Islam MT, et al., 2018). This variant is a prevalent G6PD variant in the South Asian population, typically associated with partial reduction of enzyme activity (Sarker SK, et al., 2016, Islam MT, et al., 2018). The p.Glu317Lys variant is present with allele frequency of 0.1% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic (multiple submissions). The reference amino acid change at this position on G6PD gene is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Glutamic acid at position 317 is changed to a Lysine changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

Jun 30, 2023
Baylor Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Lifecell International Pvt. Ltd
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant in exon 9 of the G6PD gene results in the amino acid substitution from glutamic acid to lysine at codon 347 (p.Glu347Lys) with the sequence change of c.1039G>A (NM_000402.4). This variant was observed in a proband with a decreased level of G6PD enzyme (3.1 U/dl) which was screened for advanced newborn screening with confirmatory genetic reflex testing at Lifecell diagnostics. There is a small physicochemical difference between glutamic acid and lysine. The observed variant is not present in both the 1000 Genomes and gnomAD databases. The reference base is conserved across the species and in-silico predictions by Polyphen and SIFT are damaging. This is a Class III variant associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only. According to the previous studies this variant is also known as G6PD Kerala, G6PD Kalyan, G6PD Kerala Kalyan, G6PD Jamnaga, and G6PD Rohini. This variant has previously been reported for Glucose-6- phosphate dehydrogenase (G6PD) deficiency by Islam MT et al., 2018. The Missense Variants Z-Score for this variant is 2.60. Missense Variants Z-Score is produced by the Exome Aggregation Consortium (60,706 adult humans) by computing a signed Z score for the deviation of observed counts from the expected number. Positive Z scores indicate increased constraint (intolerance to variation) and therefore that the gene had fewer missense variants than expected. This variant is a prevalent G6PD variant in the South Asian population, typically associated with partial reduction of enzyme activity (Ahluwalia A et al. 1992; PMID: 1303182), (Islam MT et al. 2018; PMID: 30097005), ( Ninokata A et al, 2006; PMID: 16528451), ( Sukumar S et al. 2004; PMID: 15315792), ( Sarker SK et al. 2016; PMID: 27880809), (Minucci A et al, 2012; PMID: 22293322).

May 06, 2022
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:research

Jan 01, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 317 of the G6PD protein (p.Glu317Lys). This variant is present in population databases (rs137852339, gnomAD 1.1%), and has an allele count higher than expected for a pathogenic variant. This variant is a prevalent G6PD variant in the South Asian population, typically associated with partial reduction of enzyme activity (PMID: 1303182, 30097005, 16528451, 15315792, 30097005, 27880809, 27535533). By WHO classification, this is a Class III variant associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only (PMID: 22293322). This variant is also known as G6PD Kerala, G6PD Kalyan, G6PD Kerala–Kalyan, G6PD Jamnaga, and G6PD Rohini. ClinVar contains an entry for this variant (Variation ID: 10401). 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 G6PD protein function. For these reasons, this variant has been classified as Pathogenic.

Intergen, Intergen Genetics and Rare Diseases Diagnosis Center
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

May 03, 2023
New York Genome Center
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The hemizygous, maternally inherited c.949G>A p.(Glu317Lys) variant identified in the G6PD gene substitutes an evolutionarily conserved glutamic acid with Lysine at position 317/516 (exon 9/13) in the dimer interface region [PMID: 31294066] of the encoded protein. This variant is also called c.1039G>Ap.(Glu347Lys) based on transcript NM_000402.4, and is reported in ClinVar [ClinVar ID:10401] as Pathogenic. This variant is observed in 322 alleles (0.04% minor allele frequency with 6 homozygotes and 151 hemizygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8, All of Us) including in 242 alleles(1.07% minor allele frequency with 1 homozygote and 148 hemizygotes) in South Asian subpopulation (gnomAD v2.1.1 and v3.1.2(non-Topmed)). In silico predictions are in favor of damaging effect for p.(Glu317Lys) (REVEL = 0.648). The p.(Glu317Lys) variant in G6PD has previously been reported in individuals with G6PD deficiency and is also known as G6PD Kerala, G6PD Kalyan, G6PD Kerala Kalyan, G6PD Jamnagar, and G6PD Rohini in the literature [(PMID: 15996881, 1303182, 30097005,16528451, 15315792, 27880809, 27535533, 33069889]. The c.949G>A p.(Glu317Lys) variant in G6PD is reported as Class III variant according to WHO classification and associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only [PMID:15996881,22293322]. Based on available evidence this maternally inherited hemizygous c.949G>A p.(Glu317Lys) variant identified in the G6PD gene is classified as Pathogenic.

Sep 10, 2025
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is classified as Pathogenic. Evidence in support of pathogenic classification: This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has previously been classified as a G6PD Class III variant and is known as the Kerala-Kalyan variant. Individuals with this variant have moderate to mild G6PD enzyme activity (WHO recommendations; G6PD database; PMID: 22293322; 30097005, 31833391). Additional information: Variant is predicted to result in a missense amino acid change from Glu to Lys; This variant is heterozygous; This gene is associated with X-linked recessive disease; Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (v4: 292 heterozygote(s), 7 homozygote(s), 376 hemizygote(s)); Variant is located in the annotated G6PD C-terminal domain (DECIPHER); Missense variant with conflicting in silico predictions and uninformative conservation; Loss of function is a known mechanism of disease in this gene and is associated with G6PD deficient congenital nonspherocytic haemolytic anaemia 1 (MIM#300908); This variant has been shown to be maternally inherited by trio analysis.

May 27, 2022
Mendelics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

not provided Pathogenic:4
Jun 30, 2022
Mayo Clinic Laboratories, Mayo Clinic
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Jul 13, 2022
Clinical Genetics Laboratory, Skane University Hospital Lund
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Jun 12, 2025
GeneDx
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Class III variant according to the WHO classification system, associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only (PMID: 22293322); Previously described as G6PD Kerala, G6PD Kalyan, G6PD Kerala-Kalyan, G6PD Jamnagar, and G6PD Rohini (PMID: 1303182, 15996881); This variant is associated with the following publications: (PMID: 32036089, 30097005, 36508454, 34551338, 34620237, 33069889, 20713184, 27880809, 27535533, 17233850, 1303182, 15996881, 22293322, 36681081, 38312194, 38488835)

Jul 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

G6PD: PP1:Strong, PS4, PS3:Moderate

G6PD deficiency Pathogenic:2
Mar 05, 2021
Illumina Laboratory Services, Illumina
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The G6PD c.1039G>A (p. Glu347Lys) missense variant, which is also commonly reported as c.949G>A (p.Glu317Lys) and G6PD Kerala-Kalyan, and less commonly reported as G6PD Jamnagar or Rohini, is one of the most common disease-causing variants in South Asian populations. The p.Glu347Lys variant has been estimated to account for between 1.1% and 24.5% of disease-causing alleles in the Indian population (Sukumar et al. 2004; Devendra et al. 2020). This variant has also been reported in affected individuals of Bangladeshi, Burmese, and Thai descent (Nuchprayoon et al. 2008; Sarker et al. 2016). The p.Glu347Lys variant is typically associated with glucose-6-phosphate dehydrogenase enzyme activity levels between 10% - 60% of wild type and is considered a class III variant according the WHO classification system for G6PD variants (Minucci et al. 2012; Harcke et al. 2019). The p.Glu347Lys variant is reported at a frequency of 0.01138 in the South Asian population of the Genome Aggregation Database. This allele frequency is high but is consistent with the disease prevalence estimates. Although the consequences of p.Glu347Lys have not been characterized experimentally, the Glu347 residue is known to interact with Lys275, which is the site of the another disease-causing variant, p.Lys275Asn or G6PD Bangkok. This interaction forms a salt bridge between subunits B and C of the tetrameric structure in wild-type G6PD (Boonyuen et al. 2017). Based on the collective evidence and application of the ACMG criteria, the p. Glu347Lys variant is classified as pathogenic for glucose-6-phosphate dehydrogenase deficiency.

May 22, 2025
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Variant summary: G6PD c.1039G>A (p.Glu347Lys) results in a conservative amino acid change in the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change. The variant allele was found at a frequency of 0.0012 in 183230 control chromosomes in the gnomAD database, including 1 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in G6PD causing Glucose 6 Phosphate Dehydrogenase Deficiency (0.0012 vs 0.29), allowing no conclusion about variant significance. c.1039G>A (also known as G6PD Kerala-Kalyan) has been observed in multiple individuals affected with Glucose 6 Phosphate Dehydrogenase Deficiency (example: Sukumar_2004). 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: 15315792). ClinVar contains an entry for this variant (Variation ID: 10401). Based on the evidence outlined above, the variant was classified as pathogenic.

Malaria, susceptibility to;C2720289:Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:1
Apr 06, 2024
Fulgent Genetics, Fulgent Genetics
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Malaria, susceptibility to Pathogenic:1
Mar 16, 2024
Baylor Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Congenital nonspherocytic hemolytic anemia Pathogenic:1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:research

No clinically relevant variants in concordance with the observed phenotype were found in proband. However, a known missense variant, c.949G>A p.(Glu317Lys) in exon 9 of G6PD (NM_001360016.2) was observed in hemizygous state in the proband (Arunachalam et al., 2019; Minucci et al., 2012). Sanger validation and segregation analysis showed that the variant is found in hemizygous state in the proband, heterozygous state in his mother (Lab ID-10044) and absent in his father (Lab ID-10045). This variant is present in 682 individuals in heterozygous state, 376 individuals in hemizygous state, and 7 individuals in homozygous state in gnomAD (v4.1.0). Also, the variant is present in 41 individuals in heterozygous state and 23 individuals in hemizygous/homozygous state in our in-house database of 3464 exomes. Individuals with disease-causing variants in G6PD may be asymptomatic, however may develop severe hemolysis when exposed to oxidative agents which include certain foods and medications.

G6PD KERALA Other:1
Apr 18, 2013
OMIM
Significance:other
Review Status:no assertion criteria provided
Collection Method:literature only

G6PD KERALA-KALYAN Other:1
Apr 18, 2013
OMIM
Significance:other
Review Status:no assertion criteria provided
Collection Method:literature only

G6PD KALYAN Other:1
Apr 18, 2013
OMIM
Significance:other
Review Status:no assertion criteria provided
Collection Method:literature only

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Pathogenic
0.41
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.86
D
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.88
D
MetaRNN
Benign
0.013
T
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Benign
1.2
L
PhyloP100
2.8
PrimateAI
Benign
0.46
T
PROVEAN
Uncertain
-3.7
D
REVEL
Pathogenic
0.65
Sift
Uncertain
0.0010
D
Sift4G
Benign
0.32
T
Polyphen
0.84
P
Vest4
0.51
MutPred
0.84
Gain of ubiquitination at E317 (P = 0.0048)
MVP
1.0
MPC
1.2
ClinPred
0.073
T
GERP RS
5.5
Varity_R
0.77
gMVP
0.89
Mutation Taster
=63/37
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: rs137852339; hg19: chrX-153761259; COSMIC: COSV104423998; COSMIC: COSV104423998; API