NM_015506.3(MMACHC):c.688C>T (p.Arg230Ter) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 7, 2022
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:: RCV000579162.3

Allele description [Variation Report for NM_015506.3(MMACHC):c.688C>T (p.Arg230Ter)]

NM_015506.3(MMACHC):c.688C>T (p.Arg230Ter)

Genes:

LOC129930446:ATAC-STARR-seq lymphoblastoid active region 972 [Gene]
MMACHC:metabolism of cobalamin associated C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.1

Genomic location:

Preferred name:

NM_015506.3(MMACHC):c.688C>T (p.Arg230Ter)

HGVS:

NC_000001.11:g.45509054C>T
NG_013378.1:g.13871C>T
NM_001330540.2:c.517C>T
NM_015506.3:c.688C>TMANE SELECT
NP_001317469.1:p.Arg173Ter
NP_056321.2:p.Arg230Ter
NC_000001.10:g.45974726C>T
NM_015506.2:c.688C>T

Protein change:

R173*

Links:

dbSNP: rs201183360

NCBI 1000 Genomes Browser:

rs201183360

Molecular consequence:

NM_001330540.2:c.517C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_015506.3:c.688C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000680549	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Sep 7, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000680549

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Sep 7, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000680549.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 52 amino acids are lost; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31589614, 22642810, 26990548)

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

Last Updated: May 25, 2025

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