20-34560954-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080476.5(PIGU):āc.1220A>Gā(p.Tyr407Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000521 in 1,611,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 33)
Exomes š: 0.000053 ( 0 hom. )
Consequence
PIGU
NM_080476.5 missense
NM_080476.5 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 5.26
Genes affected
PIGU (HGNC:15791): (phosphatidylinositol glycan anchor biosynthesis class U) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Cdc91, a predicted integral membrane protein that may function in cell division control. The protein encoded by this gene is the fifth subunit of GPI transamidase that attaches GPI-anchors to proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2516116).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGU | NM_080476.5 | c.1220A>G | p.Tyr407Cys | missense_variant | 12/12 | ENST00000217446.8 | |
PIGU | XM_017027664.2 | c.1076A>G | p.Tyr359Cys | missense_variant | 11/11 | ||
PIGU | XM_011528542.2 | c.572A>G | p.Tyr191Cys | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGU | ENST00000217446.8 | c.1220A>G | p.Tyr407Cys | missense_variant | 12/12 | 1 | NM_080476.5 | P1 | |
PIGU | ENST00000374820.6 | c.1160A>G | p.Tyr387Cys | missense_variant | 11/11 | 1 | |||
PIGU | ENST00000438215.1 | c.458A>G | p.Tyr153Cys | missense_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152164Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000132 AC: 33AN: 250448Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135364
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GnomAD4 exome AF: 0.0000528 AC: 77AN: 1459594Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 726286
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74458
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | This variant is present in population databases (rs202231071, gnomAD 0.02%). This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 407 of the PIGU protein (p.Tyr407Cys). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1442103). This variant has not been reported in the literature in individuals affected with PIGU-related conditions. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;.
Polyphen
D;D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at