NM_000159.4(GCDH):c.1244-2A>C AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 14, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000521145.6

Allele description [Variation Report for NM_000159.4(GCDH):c.1244-2A>C]

NM_000159.4(GCDH):c.1244-2A>C

Genes:

LOC126862860:BRD4-independent group 4 enhancer GRCh37_chr19:13010146-13011345 [Gene]
GCDH:glutaryl-CoA dehydrogenase [Gene - OMIM - HGNC]
SYCE2:synaptonemal complex central element protein 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.13

Genomic location:

Preferred name:

NM_000159.4(GCDH):c.1244-2A>C

HGVS:

NC_000019.10:g.12899466A>C
NG_009292.1:g.13307A>C
NG_033049.1:g.24807T>G
NG_087357.1:g.235A>C
NM_000159.4:c.1244-2A>CMANE SELECT
NM_001105578.2:c.613-81T>GMANE SELECT
NM_013976.5:c.1244-234A>C
NC_000019.9:g.13010280A>C
NM_000159.2:c.1244-2A>C
NM_000159.3:c.1244-2A>C

Links:

dbSNP: rs199999619

NCBI 1000 Genomes Browser:

rs199999619

Molecular consequence:

NM_001105578.2:c.613-81T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_013976.5:c.1244-234A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000159.4:c.1244-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000225488	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Sep 10, 2018)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11058907, 18683078, 21176883, 27672653 Citation Link,
SCV000617681	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000225488

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Pathogenic
(Sep 10, 2018)

germline

clinical testing

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

Citation Link,

SCV000617681

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 14, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Recurrent and novel mutations of GCDH gene in Chinese glutaric acidemia type I families.

Tang NL, Hui J, Law LK, Lam YY, Chan KY, Yeung WL, Chan AY, Cheung KL, Fok TF.

Hum Mutat. 2000 Nov;16(5):446.

PubMed [citation]

PMID:: 11058907

Glutaric aciduria type I: outcome following detection by newborn screening.

Bijarnia S, Wiley V, Carpenter K, Christodoulou J, Ellaway CJ, Wilcken B.

J Inherit Metab Dis. 2008 Aug;31(4):503-7. doi: 10.1007/s10545-008-0912-z. Epub 2008 Aug 9.

PubMed [citation]

PMID:: 18683078

See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000225488.5

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV000617681.3

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

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 18683078, 27672653, 15505393, 29419857, 29961769, 30298489, 32508882, 32005694, 35231114, 35095998, 34344405, 11058907)

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

Last Updated: Nov 30, 2024

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