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NM_022132.5(MCCC2):c.838G>T (p.Asp280Tyr)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: May 13, 2021)
Last evaluated:
May 13, 2021
Accession:
VCV000001927.5
Variation ID:
1927
Description:
single nucleotide variant
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NM_022132.5(MCCC2):c.838G>T (p.Asp280Tyr)

Allele ID
16966
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q13.2
Genomic location
5: 71634977 (GRCh38) GRCh38 UCSC
5: 70930804 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.71634977G>T
NC_000005.9:g.70930804G>T
NM_022132.5:c.838G>T MANE Select NP_071415.1:p.Asp280Tyr missense
... more HGVS
Protein change
D280Y, D242Y
Other names
-
Canonical SPDI
NC_000005.10:71634976:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00006
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00004
Links
ClinGen: CA251973
UniProtKB: Q9HCC0#VAR_067199
OMIM: 609014.0009
dbSNP: rs119103226
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, multiple submitters, no conflicts May 13, 2021 RCV000002004.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MCCC2 - - GRCh38
GRCh38
GRCh38
GRCh37
382 392

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Aug 21, 2020)
criteria provided, single submitter
Method: clinical testing
3-methylcrotonyl CoA carboxylase 2 deficiency
Allele origin: germline
Invitae
Accession: SCV000955887.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces aspartic acid with tyrosine at codon 280 of the MCCC2 protein (p.Asp280Tyr). The aspartic acid residue is highly conserved and there … (more)
Likely pathogenic
(May 13, 2021)
criteria provided, single submitter
Method: clinical testing
3-methylcrotonyl CoA carboxylase 2 deficiency
Allele origin: germline
Genetics and Prenatal Diagnosis Center,The First Affiliated Hospital of Zhengzhou University
Accession: SCV001622419.1
Submitted: (May 13, 2021)
Comment:
The heterozygous variants in MCCC2 gene c.592C>T (p. Gln198*) and c.838G>T (p. Asp280Tyr) were identified in a patient.
Evidence details
Pathogenic
(Jan 01, 2007)
no assertion criteria provided
Method: literature only
3-@METHYLCROTONYL-CoA CARBOXYLASE 2 DEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000022162.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Maternal 3-methylcrotonyl-coenzyme A carboxylase deficiency with elevated 3-hydroxyisovalerylcarnitine in breast milk. Cho KL Korean journal of pediatrics 2016 PMID: 28018443
Mutational spectrum in eight Korean patients with 3-methylcrotonyl-CoA carboxylase deficiency. Cho SY Clinical genetics 2012 PMID: 22150417
Uneventful clinical courses of Korean patients with methylcrotonylglycinuria and their common mutations. Jung CW Journal of human genetics 2012 PMID: 22030835
Novel mutations in five Japanese patients with 3-methylcrotonyl-CoA carboxylase deficiency. Uematsu M Journal of human genetics 2007 PMID: 17968484

Text-mined citations for rs119103226...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 20, 2021