rs751914635
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PVS1_ModerateBS2_Supporting
The NM_005912.3(MC4R):c.983T>A(p.Leu328*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000041 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005912.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MC4R | ENST00000299766.5 | c.983T>A | p.Leu328* | stop_gained | Exon 1 of 1 | 6 | NM_005912.3 | ENSP00000299766.3 | ||
ENSG00000285681 | ENST00000650201.1 | n.113+42022A>T | intron_variant | Intron 1 of 3 | ||||||
ENSG00000285681 | ENST00000658928.1 | n.156+42022A>T | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251414Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135870
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:2
This sequence change creates a premature translational stop signal (p.Leu328*) in the MC4R gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 5 amino acid(s) of the MC4R protein. This variant is present in population databases (rs751914635, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with clinical features of obesity (PMID: 29991773, 32952152). ClinVar contains an entry for this variant (Variation ID: 586139). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal does not substantially affect MC4R function (PMID: 29991773). 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. -
Available data are insufficient to determine the clinical significance of the variant at this time. The available data on the frequency of this variant in large general population databases was not informative towards the evaluation of its pathogenicity. (http://gnomad.broadinstitute.org) MC4R is a single-exon gene and therefore splicing is not expected, nor predicted. Assessment of experimental evidence regarding the effect of this variant on protein function suggests it has no effect relevant to disease. The variant is reported to display normal cell surface localization and normal signal transduction in response to ligand binding (PMID: 29991773) -
MC4R-related disorder Uncertain:1
The MC4R c.983T>A variant is predicted to result in premature protein termination (p.Leu328*). This variant truncates the final five amino acids of the MC4R protein. To our knowledge, this variant has not been reported in individuals with MC4R-related disease. This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/18-58038600-A-T). Although truncating variants are expected to be pathogenic, to our knowledge, all are located upstream of this variant. In ClinVar, this variant has been interpreted as pathogenic (https://ncbi.nlm.nih.gov/clinvar/variation/586139/). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at