rs398124254

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

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 7.40
Variant links:
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
MLYCDNM_012213.3 linkuse as main transcriptc.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
MLYCDENST00000262430.6 linkuse as main transcriptc.680_685dup p.Lys228_Arg229insLeuLys inframe_insertion 3/51 NM_012213.3 ENSP00000262430 P1O95822-1
MLYCDENST00000561562.5 linkuse as main transcriptc.33_38dup p.Lys13_Arg14insLeuLys inframe_insertion 1/42 ENSP00000484042
MLYCDENST00000563312.5 linkuse as main transcript upstream_gene_variant 2 ENSP00000477143
MLYCDENST00000566309.2 linkuse as main transcript upstream_gene_variant 2 ENSP00000476300

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
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 providedclinical testingEurofins Ntd Llc (ga)Jan 21, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs398124254; hg19: chr16-83941768; API