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NM_000156.6(GAMT):c.24del (p.Ile9fs) AND GAMT-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 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:
RCV003413863.4

Allele description [Variation Report for NM_000156.6(GAMT):c.24del (p.Ile9fs)]

NM_000156.6(GAMT):c.24del (p.Ile9fs)

Genes:
LOC130062945:ATAC-STARR-seq lymphoblastoid silent region 9707 [Gene]
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000156.6(GAMT):c.24del (p.Ile9fs)
HGVS:
  • NC_000019.10:g.1401457del
  • NG_009785.1:g.5101del
  • NM_000156.6:c.24delMANE SELECT
  • NM_138924.3:c.24del
  • NP_000147.1:p.Ile9fs
  • NP_620279.1:p.Ile9fs
  • NC_000019.9:g.1401452del
  • NC_000019.9:g.1401456del
  • NM_000156.4:c.24del
  • NM_000156.5:c.24del
  • NM_000156.5:c.24delC
  • NM_000156.6:c.24del
  • NM_000156.6:c.24delCMANE SELECT
Protein change:
I9fs
Links:
dbSNP: rs967689898
NCBI 1000 Genomes Browser:
rs967689898
Molecular consequence:
  • NM_000156.6:c.24del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_138924.3:c.24del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
GAMT-related disorder
Synonyms:
GAMT-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004116713PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jul 31, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot 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 PreventionGenetics, part of Exact Sciences, SCV004116713.1

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

Description

The GAMT c.24delC variant is predicted to result in a frameshift and premature protein termination (p.Ile9Serfs*33). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.021% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/19-1401451-TG-T). Frameshift variants in GAMT are expected to be pathogenic (see, for example, Item et al. 2004. PubMed ID: 15108290). In ClinVar, this variant is interpreted as pathogenic/likely pathogenic by multiple laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/850261/). This variant is interpreted as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024