U.S. flag

An official website of the United States government

NM_000156.6(GAMT):c.167C>T (p.Ala56Val) AND Deficiency of guanidinoacetate methyltransferase

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 30, 2021
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:
RCV002060782.2

Allele description [Variation Report for NM_000156.6(GAMT):c.167C>T (p.Ala56Val)]

NM_000156.6(GAMT):c.167C>T (p.Ala56Val)

Genes:
LOC130062945:ATAC-STARR-seq lymphoblastoid silent region 9707 [Gene]
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000156.6(GAMT):c.167C>T (p.Ala56Val)
HGVS:
  • NC_000019.10:g.1401310G>A
  • NG_009785.1:g.5244C>T
  • NM_000156.6:c.167C>TMANE SELECT
  • NM_138924.3:c.167C>T
  • NP_000147.1:p.Ala56Val
  • NP_620279.1:p.Ala56Val
  • NC_000019.9:g.1401309G>A
  • NM_000156.5:c.167C>T
Protein change:
A56V
Links:
dbSNP: rs575350720
NCBI 1000 Genomes Browser:
rs575350720
Molecular consequence:
  • NM_000156.6:c.167C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138924.3:c.167C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Deficiency of guanidinoacetate methyltransferase (CCDS2)
Synonyms:
CEREBRAL CREATINE DEFICIENCY SYNDROME 2
Identifiers:
MONDO: MONDO:0012999; MedGen: C0574080; Orphanet: 382; OMIM: 612736

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
SCV002495784Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 30, 2021) 		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 Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV002495784.2

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

Description

GAMT NM_000156.5 exon 1 p.Ala56Val (c.167C>T): This variant has not been reported in the literature but is present in 0.02% (3/13658) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/19-1401310-G-A?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:544255). This variant amino acid Valine (Val) is present in >30 species including mammals and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Sep 29, 2024