NM_005566.4(LDHA):c.7A>G (p.Thr3Ala) AND Glycogen storage disease due to lactate dehydrogenase M-subunit deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 11, 2023
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:: RCV003090546.3

Allele description [Variation Report for NM_005566.4(LDHA):c.7A>G (p.Thr3Ala)]

NM_005566.4(LDHA):c.7A>G (p.Thr3Ala)

Gene:

LDHA:lactate dehydrogenase A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.1

Genomic location:

Preferred name:

NM_005566.4(LDHA):c.7A>G (p.Thr3Ala)

HGVS:

NC_000011.10:g.18396849A>G
NG_008185.1:g.7415A>G
NM_001135239.2:c.7A>G
NM_001165414.2:c.94A>G
NM_001165415.2:c.7A>G
NM_001165416.2:c.7A>G
NM_005566.4:c.7A>GMANE SELECT
NP_001128711.1:p.Thr3Ala
NP_001158886.1:p.Thr32Ala
NP_001158887.1:p.Thr3Ala
NP_001158888.1:p.Thr3Ala
NP_005557.1:p.Thr3Ala
NC_000011.9:g.18418396A>G
NR_028500.2:n.105A>G

Protein change:

T32A

Molecular consequence:

NM_001135239.2:c.7A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001165414.2:c.94A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001165415.2:c.7A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001165416.2:c.7A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005566.4:c.7A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_028500.2:n.105A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
Synonyms:: GSD XI; LACTATE DEHYDROGENASE A DEFICIENCY; Glycogen storage disease XI
Identifiers:: MONDO: MONDO:0013047; MedGen: C2931743; Orphanet: 284426; OMIM: 612933

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003488329	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 11, 2023)	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

SCV003488329

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 11, 2023)

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, SCV003488329.2

#	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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The alanine 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: 2172379). This variant has not been reported in the literature in individuals affected with LDHA-related conditions. This variant is present in population databases (rs375339263, gnomAD 0.003%). This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 3 of the LDHA protein (p.Thr3Ala).

#	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: Oct 8, 2024

ClinVar

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