NM_001258392.3(CLPB):c.214G>A (p.Gly72Arg) AND 3-methylglutaconic aciduria, type VIIB

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 1, 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:: RCV000798130.8

Allele description [Variation Report for NM_001258392.3(CLPB):c.214G>A (p.Gly72Arg)]

NM_001258392.3(CLPB):c.214G>A (p.Gly72Arg)

Genes:

LOC130006336:ATAC-STARR-seq lymphoblastoid active region 5191 [Gene]
CLPB:ClpB family mitochondrial disaggregase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_001258392.3(CLPB):c.214G>A (p.Gly72Arg)

HGVS:

NC_000011.10:g.72434261C>T
NG_042130.2:g.5424G>A
NM_001258392.3:c.214G>AMANE SELECT
NM_001258393.3:c.214G>A
NM_001258394.3:c.-29G>A
NM_030813.6:c.214G>A
NP_001245321.1:p.Gly72Arg
NP_001245322.1:p.Gly72Arg
NP_110440.1:p.Gly72Arg
LRG_1338t1:c.214G>A
LRG_1338:g.5424G>A
LRG_1338p1:p.Gly72Arg
NC_000011.9:g.72145305C>T
NM_030813.5:c.214G>A

Protein change:

G72R

Links:

dbSNP: rs758376345

NCBI 1000 Genomes Browser:

rs758376345

Molecular consequence:

NM_001258394.3:c.-29G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258392.3:c.214G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258393.3:c.214G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_030813.6:c.214G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: 3-methylglutaconic aciduria, type VIIB (MGCA7B)
Synonyms:: 3-methylglutaconic aciduria with cataracts, neurologic involvement and neutropenia; 3-methylglutaconic aciduria, type VII, with cataracts, neurologic involvement and neutropenia
Identifiers:: MONDO: MONDO:0014561; MedGen: C5676893; Orphanet: 445038; OMIM: 616271

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000937729	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000937729

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 1, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000937729.5

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 644249). This variant has not been reported in the literature in individuals affected with CLPB-related conditions. This variant is present in population databases (rs758376345, gnomAD 0.008%). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 72 of the CLPB protein (p.Gly72Arg).

#	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: Sep 29, 2024

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