NM_021971.4(GMPPB):c.938G>T (p.Arg313Leu) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 31, 2021
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:: RCV001935735.5

Allele description [Variation Report for NM_021971.4(GMPPB):c.938G>T (p.Arg313Leu)]

NM_021971.4(GMPPB):c.938G>T (p.Arg313Leu)

Gene:

GMPPB:GDP-mannose pyrophosphorylase B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_021971.4(GMPPB):c.938G>T (p.Arg313Leu)

HGVS:

NC_000003.12:g.49721978C>A
NG_011603.1:g.37422C>A
NG_033731.1:g.6997G>T
NG_033731.2:g.6997G>T
NM_013334.4:c.938G>T
NM_021971.4:c.938G>TMANE SELECT
NP_037466.3:p.Arg313Leu
NP_068806.2:p.Arg313Leu
NC_000003.11:g.49759411C>A

Protein change:

R313L

Links:

dbSNP: rs775910135

NCBI 1000 Genomes Browser:

rs775910135

Molecular consequence:

NM_013334.4:c.938G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021971.4:c.938G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14
Synonyms:: WALKER-WARBURG SYNDROME OR MUSCLE-EYE-BRAIN DISEASE, GMPPB-RELATED; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 14; Congenital Muscular Dystrophy-Dystroglycanopathy with Brain and Eye Anomalies Type A 14; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0014140; MedGen: C3809216; Orphanet: 588; OMIM: 615350

Name:: Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14 (MDDGB14)
Synonyms:: MUSCULAR DYSTROPHY, CONGENITAL, GMPPB-RELATED; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B14; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 14
Identifiers:: MONDO: MONDO:0014141; MedGen: C3809221; OMIM: 615351

Name:: Autosomal recessive limb-girdle muscular dystrophy type 2T
Synonyms:: MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY, LIMB-GIRDLE, GMPPB-RELATED; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2T; Muscular dystrophy-dystroglycanopathy (limb-girdle), type c, 14; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0014142; MedGen: C4518000; Orphanet: 363623; OMIM: 615352

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002195747	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 31, 2021)	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

SCV002195747

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 31, 2021)

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, SCV002195747.2

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

Description

This sequence change replaces arginine with leucine at codon 313 of the GMPPB protein (p.Arg313Leu). The arginine residue is weakly conserved and there is a moderate physicochemical difference between arginine and leucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with GMPPB-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GMPPB protein function. 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.

#	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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