chr20-45416269-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_015937.6(PIGT):​c.113C>T​(p.Pro38Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PIGT
NM_015937.6 missense

Scores

7
11
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.92
Variant links:
Genes affected
PIGT (HGNC:14938): (phosphatidylinositol glycan anchor biosynthesis class T) This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This protein is an essential component of the multisubunit enzyme, GPI transamidase. GPI transamidase mediates GPI anchoring in the endoplasmic reticulum, by catalyzing the transfer of fully assembled GPI units to proteins. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.919

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PIGTNM_015937.6 linkuse as main transcriptc.113C>T p.Pro38Leu missense_variant 1/12 ENST00000279036.12 NP_057021.2
LOC107985405XR_001754640.2 linkuse as main transcriptn.719G>A non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIGTENST00000279036.12 linkuse as main transcriptc.113C>T p.Pro38Leu missense_variant 1/121 NM_015937.6 ENSP00000279036 P1Q969N2-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1442294
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
715796
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:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Multiple congenital anomalies-hypotonia-seizures syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJul 07, 2023ClinVar contains an entry for this variant (Variation ID: 1945195). This variant has not been reported in the literature in individuals affected with PIGT-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 38 of the PIGT protein (p.Pro38Leu). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PIGT protein function. 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.060
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.47
T;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Eigen
Pathogenic
0.76
Eigen_PC
Pathogenic
0.68
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.95
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Uncertain
0.14
D
MetaRNN
Pathogenic
0.92
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
-0.025
T
MutationAssessor
Pathogenic
3.7
H;H;H;H;.;.;.;.;.;.;.;.;.;H;.
MutationTaster
Benign
1.0
D;D;D;D;D;D
PrimateAI
Pathogenic
0.79
T
PROVEAN
Pathogenic
-8.3
D;N;D;D;.;.;.;.;.;.;.;.;.;D;.
REVEL
Uncertain
0.42
Sift
Uncertain
0.0010
D;D;D;D;.;.;.;.;.;.;.;.;.;D;.
Sift4G
Uncertain
0.0070
D;D;D;D;.;.;.;.;.;.;.;.;.;.;.
Polyphen
1.0
D;D;.;.;.;.;.;.;.;.;.;.;.;D;.
Vest4
0.72
MutPred
0.85
Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);Loss of catalytic residue at P38 (P = 0.0645);.;
MVP
0.76
MPC
0.51
ClinPred
1.0
D
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.0
Varity_R
0.84
gMVP
0.83

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1218912444; hg19: chr20-44044909; API