NM_000159.4(GCDH):c.109C>T (p.Gln37Ter) AND Glutaric aciduria, type 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 31, 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:: RCV003499499.2

Allele description [Variation Report for NM_000159.4(GCDH):c.109C>T (p.Gln37Ter)]

NM_000159.4(GCDH):c.109C>T (p.Gln37Ter)

Genes:

LOC117125594:CRISPRi-FlowFISH-validated KLF1 regulatory element [Gene]
GCDH:glutaryl-CoA dehydrogenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.13

Genomic location:

Preferred name:

NM_000159.4(GCDH):c.109C>T (p.Gln37Ter)

HGVS:

NC_000019.10:g.12891504C>T
NG_009292.1:g.5345C>T
NG_013087.1:g.700G>A
NG_068132.2:g.938C>T
NM_000159.4:c.109C>TMANE SELECT
NM_013976.5:c.109C>T
NP_000150.1:p.Gln37Ter
NP_039663.1:p.Gln37Ter
LRG_825:g.700G>A
NC_000019.9:g.13002318C>T
NR_102316.1:n.217C>T
NR_102317.1:n.217C>T

Protein change:

Q37*

Molecular consequence:

NR_102316.1:n.217C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_102317.1:n.217C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000159.4:c.109C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_013976.5:c.109C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Glutaric aciduria, type 1
Synonyms:: GA I; Glutaryl-CoA dehydrogenase deficiency; Glutaric acidemia type I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009281; MedGen: C0268595; Orphanet: 25; OMIM: 231670

Recent activity

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recombination activating gene 1, partial [Hipposideros ater]
recombination activating gene 1, partial [Hipposideros ater]
gi|2329595850|gb|UZO68844.1|

Protein
Abnormal labia morphology
Abnormal labia morphology

MedGen
HKC8_0.5_6hr_HIF2a_rep1
HKC8_0.5_6hr_HIF2a_rep1

GEO DataSets

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004338139	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 31, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10699052, 11854167, 16602100, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004338139

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 31, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Mutation analysis in glutaric aciduria type I.

Zschocke J, Quak E, Guldberg P, Hoffmann GF.

J Med Genet. 2000 Mar;37(3):177-81.

PubMed [citation]

PMID:: 10699052
PMCID:: PMC1734541

Biochemical, pathologic and behavioral analysis of a mouse model of glutaric acidemia type I.

Koeller DM, Woontner M, Crnic LS, Kleinschmidt-DeMasters B, Stephens J, Hunt EL, Goodman SI.

Hum Mol Genet. 2002 Feb 15;11(4):347-57.

PubMed [citation]

PMID:: 11854167

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004338139.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gln37*) in the GCDH gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GCDH are known to be pathogenic (PMID: 10699052, 11854167, 16602100). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GCDH-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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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