NM_001370259.2:c.466G>T
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_001370259.2(MEN1):c.466G>T(p.Gly156Cys) 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G156D) has been classified as Pathogenic.
Frequency
Consequence
NM_001370259.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEN1 | NM_001370259.2 | c.466G>T | p.Gly156Cys | missense_variant | Exon 3 of 10 | ENST00000450708.7 | NP_001357188.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Multiple endocrine neoplasia, type 1 Pathogenic:1
This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 156 of the MEN1 protein (p.Gly156Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with primary hyperparathyroidism (PMID: 17623761). ClinVar contains an entry for this variant (Variation ID: 988303). 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 MEN1 protein function. Experimental studies have shown that this missense change affects MEN1 function (PMID: 21819486). This variant disrupts the p.Gly156 amino acid residue in MEN1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10090472, 29039523). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
not provided Pathogenic:1
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Hereditary cancer-predisposing syndrome Pathogenic:1
The p.G156C pathogenic mutation (also known as c.466G>T), located in coding exon 2 of the MEN1 gene, results from a G to T substitution at nucleotide position 466. The glycine at codon 156 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been detected in unrelated individuals with hyperparathyroidism and other clinical features of MEN1 (Tham E et al. J. Clin. Endocrinol. Metab., 2007 Sep;92:3389-95; Ambry Internal Data). Functional analysis showed steady state protein expression to be less than 20% of wild type using immunocytochemical assays (Shimazu S et al. Cancer Sci., 2011 Nov;102:2097-102). In addition, several other missense alterations at this same codon (G156D, G156S, G156V, and G156R) have been described in patients with clinical diagnosis of MEN1 (Vierimaa O et al. Eur. J. Endocrinol., 2007 Sep;157:285-94; Belar O et al. Clin. Endocrinol. (Oxf), 2012 May;76:719-24; Tham E et al. J. Clin. Endocrinol. Metab., 2007 Sep;92:3389-95; Mutch MG et al. Hum. Mutat., 1999;13:175-85). Based on the available evidence, this alteration is classified as a pathogenic mutation. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at