rs398124254
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The ENST00000262430.6(MLYCD):c.680_685dup(p.Lys228_Arg229insLeuLys) variant causes a inframe insertion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
MLYCD
ENST00000262430.6 inframe_insertion
ENST00000262430.6 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.40
Genes affected
MLYCD (HGNC:7150): (malonyl-CoA decarboxylase) The product of this gene catalyzes the breakdown of malonyl-CoA to acetyl-CoA and carbon dioxide. Malonyl-CoA is an intermediate in fatty acid biosynthesis, and also inhibits the transport of fatty acyl CoAs into mitochondria. Consequently, the encoded protein acts to increase the rate of fatty acid oxidation. It is found in mitochondria, peroxisomes, and the cytoplasm. Mutations in this gene result in malonyl-CoA decarboyxlase deficiency. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in ENST00000262430.6.
PP5
Variant 16-83908163-A-ATGAAGC is Pathogenic according to our data. Variant chr16-83908163-A-ATGAAGC is described in ClinVar as [Pathogenic]. Clinvar id is 95504.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLYCD | NM_012213.3 | c.680_685dup | p.Lys228_Arg229insLeuLys | inframe_insertion | 3/5 | ENST00000262430.6 | NP_036345.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLYCD | ENST00000262430.6 | c.680_685dup | p.Lys228_Arg229insLeuLys | inframe_insertion | 3/5 | 1 | NM_012213.3 | ENSP00000262430 | P1 | |
MLYCD | ENST00000561562.5 | c.33_38dup | p.Lys13_Arg14insLeuLys | inframe_insertion | 1/4 | 2 | ENSP00000484042 | |||
MLYCD | ENST00000563312.5 | upstream_gene_variant | 2 | ENSP00000477143 | ||||||
MLYCD | ENST00000566309.2 | upstream_gene_variant | 2 | ENSP00000476300 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Eurofins Ntd Llc (ga) | Jan 21, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at