rs782080281

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_001347217.2(WDR13):​c.582C>G​(p.Asp194Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000913 in 1,095,592 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 25)
Exomes š‘“: 9.1e-7 ( 0 hom. 0 hem. )

Consequence

WDR13
NM_001347217.2 missense

Scores

5
7
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27
Variant links:
Genes affected
WDR13 (HGNC:14352): (WD repeat domain 13) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by Gly-His and Trp-Asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. A similar protein in mouse is thought to be a negative regulator of the pancreatic beta cell proliferation. Mice lacking this gene exhibit increased pancreatic islet mass and higher serum insulin levels, and are mildly obese. [provided by RefSeq, Nov 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.973

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDR13NM_001347217.2 linkc.582C>G p.Asp194Glu missense_variant Exon 6 of 10 ENST00000376729.10 NP_001334146.1 Q9H1Z4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WDR13ENST00000376729.10 linkc.582C>G p.Asp194Glu missense_variant Exon 6 of 10 5 NM_001347217.2 ENSP00000365919.5 Q9H1Z4-1

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD4 exome
AF:
9.13e-7
AC:
1
AN:
1095592
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
361876
show subpopulations
Gnomad4 AFR exome
AF:
0.00
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:
0.0000260
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Pathogenic
0.32
D
BayesDel_noAF
Pathogenic
0.22
CADD
Benign
16
DANN
Uncertain
1.0
FATHMM_MKL
Benign
0.23
N
M_CAP
Uncertain
0.18
D
MetaRNN
Pathogenic
0.97
D;D
MetaSVM
Uncertain
-0.046
T
PrimateAI
Uncertain
0.78
T
PROVEAN
Uncertain
-3.8
D;D
REVEL
Uncertain
0.62
Sift
Uncertain
0.0030
D;D
Sift4G
Pathogenic
0.0
D;D
Vest4
0.91
MutPred
0.92
Loss of stability (P = 0.3538);Loss of stability (P = 0.3538);
MVP
0.93
MPC
2.0
ClinPred
0.98
D
GERP RS
-3.5
gMVP
0.96

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-48458765; API