rs864309742
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_015702.3(MMADHC):c.60_61insAT(p.Leu21IlefsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
MMADHC
NM_015702.3 frameshift
NM_015702.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.547
Genes affected
MMADHC (HGNC:25221): (metabolism of cobalamin associated D) This gene encodes a mitochondrial protein that is involved in an early step of vitamin B12 metabolism. Vitamin B12 (cobalamin) is essential for normal development and survival in humans. Mutations in this gene cause methylmalonic aciduria and homocystinuria type cblD (MMADHC), a disorder of cobalamin metabolism that is characterized by decreased levels of the coenzymes adenosylcobalamin and methylcobalamin. Pseudogenes have been identified on chromosomes 11 and X.[provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 33 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 2-149582220-A-AAT is Pathogenic according to our data. Variant chr2-149582220-A-AAT is described in ClinVar as [Pathogenic]. Clinvar id is 219001.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMADHC | NM_015702.3 | c.60_61insAT | p.Leu21IlefsTer2 | frameshift_variant | 3/8 | ENST00000303319.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMADHC | ENST00000303319.10 | c.60_61insAT | p.Leu21IlefsTer2 | frameshift_variant | 3/8 | 1 | NM_015702.3 | P1 | |
MMADHC | ENST00000422782.2 | c.60_61insAT | p.Leu21IlefsTer2 | frameshift_variant | 3/9 | 5 | |||
MMADHC | ENST00000428879.5 | c.60_61insAT | p.Leu21IlefsTer2 | frameshift_variant | 2/7 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Methylmalonic aciduria and homocystinuria type cblD Pathogenic:1Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Apr 09, 2019 | This variant has been observed in an individual affected with methylmalonic acidemia (PMID: 22156578). ClinVar contains an entry for this variant (Variation ID: 219001). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in MMADHC are known to be pathogenic (PMID: 18385497). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Leu21Ilefs*2) in the MMADHC gene. It is expected to result in an absent or disrupted protein product. - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at