chr12-109561053-G-A
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_052845.4(MMAB):c.571C>T(p.Arg191Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 1,510,268 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 Pathogenic (★★).
Frequency
Consequence
NM_052845.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000347 AC: 5AN: 144252Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248708Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134964
GnomAD4 exome AF: 0.0000102 AC: 14AN: 1366016Hom.: 0 Cov.: 36 AF XY: 0.00000884 AC XY: 6AN XY: 678828
GnomAD4 genome AF: 0.0000347 AC: 5AN: 144252Hom.: 0 Cov.: 30 AF XY: 0.0000286 AC XY: 2AN XY: 69908
ClinVar
Submissions by phenotype
Methylmalonic aciduria, cblB type Pathogenic:10Other:1
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 191 of the MMAB protein (p.Arg191Trp). This variant is present in population databases (rs376128990, gnomAD 0.01%). This missense change has been observed in individuals with methylmalonic aciduria cobalamin B type (PMID: 12471062, 23707710, 27591164, 30712249). ClinVar contains an entry for this variant (Variation ID: 218324). 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 MMAB protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects MMAB function (PMID: 12471062, 20556797). This variant disrupts the p.Arg191 amino acid residue in MMAB. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16410054, 23707710, 27591164; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
- -
- -
- -
- -
- -
- -
The observed missense c.571C>T(p.Arg191Trp) variant in MMAB gene has been reported previously in homozygous and compound heterozygous states in multiple individuals affected with methylmalonic aciduria cblB complementation type (Şeker Yılmaz B, et al., 2021; Keyfi F, et al., 2019; Jorge-Finnigan A, et al., 2010). Functional studies show that this variant impairs enzyme activity and affects MMAB function (Jorge-Finnigan A, et al., 2013; Zhang J, et al., 2006). The p.Arg191Trp variant has been reported with allele frequency of 0.004% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submissions). Multiple lines of computational evidences (Polyphen - Probably damaging, SIFT - Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. The amino acid change p.Arg191Trp in MMAB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 191 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. Another missense variant [c.572 G > A, p.Arg191Gln] on the same residue of this gene has previously been reported to be disease causing (Illson ML, et al., 2013), suggesting that this residue might be of clinical significance. For these reasons, this variant has been classified as Pathogenic. -
- -
- -
- -
not provided Pathogenic:2
Published functional studies found this variant is associated with significantly reduced enzyme activity (PMID: 16439175, 23674520); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 17948227, 17957493, 23674520, 16410054, 20556797, 27591164, 30022420, 30712249, 33453710, 34796408, 35712814, 29197662, 25087612, 16439175, 12471062) -
- -
Inborn genetic diseases Pathogenic:1
The c.571C>T (p.R191W) alteration is located in exon 7 (coding exon 7) of the MMAB gene. This alteration results from a C to T substitution at nucleotide position 571, causing the arginine (R) at amino acid position 191 to be replaced by a tryptophan (W). This mutation has been reported in the compound heterozygous and homozygous states in multiple individuals with methylmalonic aciduria cblB complementation type (Devi, 2017; Dobson, 2002; Lerner-Ellis, 2006; Martínez, 2005; eker Ylmaz, 2021; Shafaat, 2018). Functional studies show that this alteration impairs enzyme activity (Jorge-Finnigan, 2010; Lerner-Ellis, 2006; Zhang, 2006). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at