NM_000514.4(GDNF):c.429G>A (p.Arg143=) AND Hirschsprung disease, susceptibility to, 3

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 27, 2017
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:: RCV000264072.5

Allele description [Variation Report for NM_000514.4(GDNF):c.429G>A (p.Arg143=)]

NM_000514.4(GDNF):c.429G>A (p.Arg143=)

Gene:

GDNF:glial cell derived neurotrophic factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_000514.4(GDNF):c.429G>A (p.Arg143=)

HGVS:

NC_000005.10:g.37815858C>T
NG_011675.2:g.28823G>A
NM_000514.4:c.429G>AMANE SELECT
NM_001190468.1:c.480G>A
NM_001190469.1:c.402G>A
NM_001278098.1:c.273G>A
NM_199231.2:c.351G>A
NP_000505.1:p.Arg143=
NP_001177397.1:p.Arg160=
NP_001177398.1:p.Arg134=
NP_001265027.1:p.Arg91=
NP_954701.1:p.Arg117=
NC_000005.9:g.37815960C>T
NM_000514.3:c.429G>A
p.Arg160Arg

Links:

dbSNP: rs36010631

NCBI 1000 Genomes Browser:

rs36010631

Molecular consequence:

NM_000514.4:c.429G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001190468.1:c.480G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001190469.1:c.402G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001278098.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_199231.2:c.351G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Hirschsprung disease, susceptibility to, 3
Synonyms:: Hirschsprung disease modifier; Hirschsprung disease 3
Identifiers:: MONDO: MONDO:0013383; MedGen: C3150974; Orphanet: 388; OMIM: 613711

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000457484	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10790203, 8968758 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000457484

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link

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

RET and GDNF gene scanning in Hirschsprung patients using two dual denaturing gel systems.

Hofstra RM, Wu Y, Stulp RP, Elfferich P, Osinga J, Maas SM, Siderius L, Brooks AS, vd Ende JJ, Heydendael VM, Severijnen RS, Bax KM, Meijers C, Buys CH.

Hum Mutat. 2000;15(5):418-29.

PubMed [citation]

PMID:: 10790203

De novo mutation of GDNF, ligand for the RET/GDNFR-alpha receptor complex, in Hirschsprung disease.

Ivanchuk SM, Myers SM, Eng C, Mulligan LM.

Hum Mol Genet. 1996 Dec;5(12):2023-6.

PubMed [citation]

PMID:: 8968758

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000457484.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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: Mar 10, 2024

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