U.S. flag

An official website of the United States government

NM_004483.5(GCSH):c.425G>T (p.Gly142Val) AND Non-ketotic hyperglycinemia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 1, 2022
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:
RCV002283683.1

Allele description [Variation Report for NM_004483.5(GCSH):c.425G>T (p.Gly142Val)]

NM_004483.5(GCSH):c.425G>T (p.Gly142Val)

Gene:
GCSH:glycine cleavage system protein H [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q23.2
Genomic location:
Preferred name:
NM_004483.5(GCSH):c.425G>T (p.Gly142Val)
HGVS:
  • NC_000016.10:g.81082963C>A
  • NG_016427.1:g.18413G>T
  • NM_004483.5:c.425G>TMANE SELECT
  • NP_004474.2:p.Gly142Val
  • NP_004474.2:p.Gly142Val
  • LRG_541t1:c.425G>T
  • LRG_541:g.18413G>T
  • LRG_541p1:p.Gly142Val
  • NC_000016.9:g.81116568C>A
  • NM_004483.4:c.425G>T
  • NR_033249.2:n.478G>T
Protein change:
G142V
Molecular consequence:
  • NM_004483.5:c.425G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_033249.2:n.478G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Non-ketotic hyperglycinemia
Synonyms:
Glycine encephalopathy; Nonketotic hyperglycinemia
Identifiers:
MONDO: MONDO:0011612; MedGen: C0751748; Orphanet: 407; OMIM: PS605899; Human Phenotype Ontology: HP:0008288

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025726633billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 1, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical 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 3billion, SCV002572663.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.83; 3Cnet: 0.94). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Jun 9, 2024