NM_022132.5(MCCC2):c.891_892del (p.Lys298fs) AND 3-methylcrotonyl-CoA carboxylase 2 deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 11, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000794342.7

Allele description [Variation Report for NM_022132.5(MCCC2):c.891_892del (p.Lys298fs)]

NM_022132.5(MCCC2):c.891_892del (p.Lys298fs)

Gene:

MCCC2:methylcrotonyl-CoA carboxylase subunit 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q13.2

Genomic location:

Preferred name:

NM_022132.5(MCCC2):c.891_892del (p.Lys298fs)

HGVS:

NC_000005.10:g.71635030_71635031del
NC_000005.9:g.70930856_70930857del
NG_008882.1:g.52743_52744del
NM_001363147.1:c.777_778del
NM_022132.5:c.891_892delMANE SELECT
NP_001350076.1:p.Lys260fs
NP_071415.1:p.Lys298fs
NC_000005.9:g.70930856_70930857del
NC_000005.9:g.70930856_70930857delAG
NC_000005.9:g.70930857_70930858del
NM_022132.4:c.891_892delGA

Protein change:

K260fs

Links:

dbSNP: rs1580319814

Molecular consequence:

NM_001363147.1:c.777_778del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022132.5:c.891_892del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: 3-methylcrotonyl-CoA carboxylase 2 deficiency
Synonyms:: METHYLCROTONYLGLYCINURIA, TYPE II; 3 alpha methylcrotonyl-CoA carboxylase 2 deficiency; 3 alpha methylcrotonylglycinuria 2; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008862; MedGen: C1859499; Orphanet: 6; OMIM: 210210

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000933742	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 11, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11181649, 22642865, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000933742

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 11, 2018)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency.

Baumgartner MR, Almashanu S, Suormala T, Obie C, Cole RN, Packman S, Baumgartner ER, Valle D.

J Clin Invest. 2001 Feb;107(4):495-504.

PubMed [citation]

PMID:: 11181649
PMCID:: PMC199271

3-methylcrotonyl-CoA carboxylase deficiency: clinical, biochemical, enzymatic and molecular studies in 88 individuals.

Grünert SC, Stucki M, Morscher RJ, Suormala T, Bürer C, Burda P, Christensen E, Ficicioglu C, Herwig J, Kölker S, Möslinger D, Pasquini E, Santer R, Schwab KO, Wilcken B, Fowler B, Yue WW, Baumgartner MR.

Orphanet J Rare Dis. 2012 May 29;7:31. doi: 10.1186/1750-1172-7-31.

PubMed [citation]

PMID:: 22642865
PMCID:: PMC3495011

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000933742.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Lys298Glufs*7) in the MCCC2 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MCCC2-related disease. Loss-of-function variants in MCCC2 are known to be pathogenic (PMID: 11181649, 22642865). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 15, 2026

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