rs369841551
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_005912.3(MC4R):c.466C>T(p.Gln156*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,036 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 Likely pathogenic (★★).
Frequency
Consequence
NM_005912.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MC4R | ENST00000299766.5 | c.466C>T | p.Gln156* | stop_gained | Exon 1 of 1 | 6 | NM_005912.3 | ENSP00000299766.3 | ||
ENSG00000285681 | ENST00000650201.1 | n.113+42539G>A | intron_variant | Intron 1 of 3 | ||||||
ENSG00000285681 | ENST00000658928.1 | n.156+42539G>A | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not provided Pathogenic:4
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This sequence change creates a premature translational stop signal (p.Gln156*) in the MC4R gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 177 amino acid(s) of the MC4R protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with obesity (PMID: 30586318). ClinVar contains an entry for this variant (Variation ID: 562356). This variant disrupts a region of the MC4R protein in which other variant(s) (p.Ile301Thr) have been determined to be pathogenic (PMID: 10903341, 12690102, 16507637, 16752916, 18559663). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Identified in the heterozygous state in individuals with obesity in the published literature, however segregation studies were not completed (Vollbach et al., 2017; Namjou et al., 2021); Identified in an individual with kidney disease in the published literature, and information on body mass index was not provided (Groopman et al., 2019); Nonsense variant predicted to result in protein truncation, as the last 177 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31447099, 27654141, 29568105, 32952152, 30586318) -
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BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 20 Pathogenic:2
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Monogenic diabetes Pathogenic:1
The c.466C>T variant in codon 156 (exon 1) of the melanocortin 4 receptor gene, MC4R, results in the generation of a stop codon and the expected loss of four of the seven transmembrane domains of the protein (10592235). The c.466C>T variant was not observed in the NHLBI Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium databases. Nonsense mutations in MC4R have been reported previously as autosomal dominant, monogenic causes of obesity (10199800, 12646665). All individuals found to have pathogenic mutations in MC4R in one study had severe hyperinsulinemia, even compared to obese controls (12646665). The c.466C>T variant was previously identified in a 12-year old boy with severe early-onset obesity (27654141). Additionally, multiple lines of computational evidence (SIFT, LRT, MutationTaster, CADD, GERP) predict this variant is probably damaging to the protein structure or function. ACMG criteria = PVS1, PM2, PP3 -
Obesity Pathogenic:1
This c.466C>T (p.Gln156*) variant has not been observed in the ExAC database, nor has been observed in our patient cohort but has been reported in dbSNP (rs369841551) with a minor allele frequency of 0.00008. This c.466C>T encodes for a nonsense codon in exon 1 at amino acid position 156 of the MC4R protein. This premature stop codon is predicted to result in a loss of function of the protein. It is thus classify as a pathogenic variant. -
MC4R-related disorder Pathogenic:1
The MC4R c.466C>T variant is predicted to result in premature protein termination (p.Gln156*). This variant has been reported in an individual with obesity (Table 1, Vollbach et al. 2017. PubMed ID: 27654141; Kohlsdorf et al. 2018. PubMed ID: 29568105). Furthermore, truncating variants upstream and downstream of this variant have been reported in individuals with autosomal dominant obesity phenotypes (Farooqi et al. 2003. PubMed ID: 12646665; Wang et al. 2006. PubMed ID: 17185898). This variant has not been reported in a large population database, indicating this variant is rare. Nonsense variants in MC4R are expected to be pathogenic. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at