rs281865026
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_024312.5(GNPTAB):c.1196C>T(p.Ser399Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_024312.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNPTAB | NM_024312.5 | c.1196C>T | p.Ser399Phe | missense_variant | 10/21 | ENST00000299314.12 | NP_077288.2 | |
GNPTAB | XM_011538731.3 | c.1115C>T | p.Ser372Phe | missense_variant | 10/21 | XP_011537033.1 | ||
GNPTAB | XM_006719593.4 | c.1196C>T | p.Ser399Phe | missense_variant | 10/19 | XP_006719656.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNPTAB | ENST00000299314.12 | c.1196C>T | p.Ser399Phe | missense_variant | 10/21 | 1 | NM_024312.5 | ENSP00000299314.7 | ||
GNPTAB | ENST00000549940.5 | c.1196C>T | p.Ser399Phe | missense_variant | 10/11 | 1 | ENSP00000449150.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251402Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135872
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727216
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
Pseudo-Hurler polydystrophy Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Lifecell International Pvt. Ltd | - | A Homozygote Missense variant c.1196C>T in Exon 10 of the GNPTAB gene that results in the amino acid substitution p.Ser399Phe was identified. The variant was found in ClinVar (Variant ID: 38413) with a classification of Conflicting interpretations of pathogenicity and a review status of (1 star) criteria provided, single submitter. The observed variant has a maximum allele frequency of 0.00002/0.00003% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. The variant has been previously reported by Encarnação M, et al, 2009. Functional analysis showed the mutation leads to overexpression of the enzyme. (Qian Y et al, 2015) Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. - |
Pathogenic, no assertion criteria provided | curation | GeneReviews | May 10, 2012 | - - |
Pseudo-Hurler polydystrophy;C2673377:Mucolipidosis type II Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 399 of the GNPTAB protein (p.Ser399Phe). This variant is present in population databases (rs281865026, gnomAD 0.003%). This missense change has been observed in individual(s) with GNPTAB-related conditions (PMID: 16630736, 19659762, 23566849, 27710913). ClinVar contains an entry for this variant (Variation ID: 38413). 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 GNPTAB protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects GNPTAB function (PMID: 24375680, 24550498, 25505245). For these reasons, this variant has been classified as Pathogenic. - |
Mucolipidosis type II Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 10, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at