NM_000402.4(G6PD):c.1039G>A (p.Glu347Lys) AND 3-Methylglutaconic aciduria type 2

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Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 22, 2020
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:: RCV003225020.4

Allele description

NM_000402.4(G6PD):c.1039G>A (p.Glu347Lys)

Gene:

G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000402.4(G6PD):c.1039G>A (p.Glu347Lys)

Other names:

G6PD, GLU317LYS; G6PD Jamnaga; G6PD Kalyan; G6PD Kerala; G6PD Kerala-Kalyan; G6PD Rohini; p.Glu317Lys

HGVS:

NC_000023.11:g.154533044C>T
NG_009015.2:g.19529G>A
NM_000402.4:c.1039G>A
NM_001042351.3:c.949G>A
NM_001360016.2:c.949G>AMANE SELECT
NP_000393.4:p.Glu347Lys
NP_001035810.1:p.Glu317Lys
NP_001346945.1:p.Glu317Lys
NC_000023.10:g.153761259C>T
NM_000402.3:c.1039G>A
NM_001042351.1:c.949G>A
NM_001042351.2:c.949G>A
NM_001042351.3:c.949G>A
NM_001360016.2:c.949G>A

Protein change:

E317K; GLU317LYS

Links:

OMIM: 305900.0042; dbSNP: rs137852339

NCBI 1000 Genomes Browser:

rs137852339

Molecular consequence:

NM_000402.4:c.1039G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001042351.3:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001360016.2:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: 3-Methylglutaconic aciduria type 2 (BTHS)
Synonyms:: Barth syndrome; 3-methylglutaconicaciduria type II; MGA type II; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010543; MedGen: C0574083; Orphanet: 111; OMIM: 302060

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003921943	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 22, 2020)	maternal	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

SCV003921943

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 22, 2020)

maternal

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	maternal	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV003921943.1

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

Description

0102 - Loss of function is a known mechanism of disease in this gene and is associated with G6PD deficient hemolytic anemia (favism) (MIM#300908). (I) 0109 - This gene is associated with X-linked recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to lysine. (I) 0251 - Variant is heterozygous. (I) 0305 - Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (v2: 94 heterozygotes, 1 homozygote, 132 hemizygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated G6PD C-terminal domain (DECIPHER). (I) 0705 - No comparable variants have previous evidence for pathogenicity. (I) 0801 - Strong previous evidence of pathogenicity in unrelated individuals. This variant has previously been classified as a G6PD Class III variant and is known as the Kerala-Kalyan variant. Individuals with this variant have moderate to mild G6PD enzyme activity (WHO recommendations; G6PD database; PMID: 22293322; 30097005, 31833391). (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 15, 2024

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