NM_005276.4(GPD1):c.895G>A (p.Gly299Arg) AND Transient infantile hypertriglyceridemia and hepatosteatosis

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Dec 28, 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:: RCV001824158.3

Allele description [Variation Report for NM_005276.4(GPD1):c.895G>A (p.Gly299Arg)]

NM_005276.4(GPD1):c.895G>A (p.Gly299Arg)

Gene:

GPD1:glycerol-3-phosphate dehydrogenase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.12

Genomic location:

Preferred name:

NM_005276.4(GPD1):c.895G>A (p.Gly299Arg)

HGVS:

NC_000012.12:g.50108072G>A
NG_032155.1:g.1092G>A
NG_032168.1:g.9254G>A
NM_001257199.2:c.826G>A
NM_005276.4:c.895G>AMANE SELECT
NP_001244128.1:p.Gly276Arg
NP_005267.2:p.Gly299Arg
NC_000012.11:g.50501855G>A
NC_000012.11:g.50501855G>A

Protein change:

G276R; GLY299ARG

Links:

OMIM: 138420.0005; dbSNP: rs889092603

NCBI 1000 Genomes Browser:

rs889092603

Molecular consequence:

NM_001257199.2:c.826G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005276.4:c.895G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Transient infantile hypertriglyceridemia and hepatosteatosis
Synonyms:: Hypertriglyceridemia, transient infantile
Identifiers:: MONDO: MONDO:0013771; MedGen: C3280953; Orphanet: 300293; OMIM: 614480

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002073873	Genomics Facility, Ludwig-Maximilians-Universität München	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 28, 2021)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 22226083
SCV005049926	OMIM	no assertion criteria provided	Pathogenic (Jun 6, 2024)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002073873

Genomics Facility, Ludwig-Maximilians-Universität München

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 28, 2021)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV005049926

OMIM

no assertion criteria provided

Pathogenic
(Jun 6, 2024)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	yes	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

Transient infantile hypertriglyceridemia, fatty liver, and hepatic fibrosis caused by mutated GPD1, encoding glycerol-3-phosphate dehydrogenase 1.

Basel-Vanagaite L, Zevit N, Har Zahav A, Guo L, Parathath S, Pasmanik-Chor M, McIntyre AD, Wang J, Albin-Kaplanski A, Hartman C, Marom D, Zeharia A, Badir A, Shoerman O, Simon AJ, Rechavi G, Shohat M, Hegele RA, Fisher EA, Shamir R.

Am J Hum Genet. 2012 Jan 13;90(1):49-60. doi: 10.1016/j.ajhg.2011.11.028. Epub 2012 Jan 5.

PubMed [citation]

PMID:: 22226083
PMCID:: PMC3257852

See all PubMed Citations (3)

Details of each submission

From Genomics Facility, Ludwig-Maximilians-Universität München, SCV002073873.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

From OMIM, SCV005049926.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 9 Roma children with transient infantile hypertriglyceridemia (HTGTI; 614480), Tesarova et al. (2021) identified a homozygous c.895G-A transition in the GPD1 gene, resulting in a gly299-to-arg (G299R) substitution. None of the parents or healthy sibs carried the variant in homozygous state. The authors suggested a founder effect of this variant in the Roma population. The variant was not present in the gnomAD database.

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

Last Updated: Oct 8, 2024

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