NM_000156.6(GAMT):c.172TCC[3] (p.Ser59dup) AND Cerebral creatine deficiency syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 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:: RCV000793456.4

Allele description [Variation Report for NM_000156.6(GAMT):c.172TCC[3] (p.Ser59dup)]

NM_000156.6(GAMT):c.172TCC[3] (p.Ser59dup)

Genes:

LOC130062945:ATAC-STARR-seq lymphoblastoid silent region 9707 [Gene]
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_000156.6(GAMT):c.172TCC[3] (p.Ser59dup)

HGVS:

NC_000019.10:g.1401302AGG[3]
NG_009785.1:g.5249TCC[3]
NM_000156.6:c.172TCC[3]MANE SELECT
NM_138924.1:c.175_177dupTCC
NM_138924.3:c.172TCC[3]
NP_000147.1:p.Ser59dup
NP_620279.1:p.Ser59dup
NC_000019.9:g.1401298_1401299insGGA
NC_000019.9:g.1401301AGG[3]
NM_000156.4:c.175_177dup
NM_000156.5:c.175_177dup
NM_000156.5:c.175_177dupTCC
NM_000156.6:c.175_177dupMANE SELECT
NM_000156.6:c.175_177dupTCCMANE SELECT

Links:

dbSNP: rs768895098

NCBI 1000 Genomes Browser:

rs768895098

Molecular consequence:

NM_000156.6:c.172TCC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_138924.3:c.172TCC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Name:: Cerebral creatine deficiency syndrome (CCAD)
Synonyms:: Creatine deficiency syndromes
Identifiers:: MONDO: MONDO:0000456; MedGen: C5244016; Orphanet: 79172; OMIM: PS300352

Recent activity

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Homo sapiens BCL11 transcription factor A (BCL11A), transcript variant 3, mRNA
Homo sapiens BCL11 transcription factor A (BCL11A), transcript variant 3, mRNA
gi|1677502074|ref|NM_138559.2|

Nucleotide
SPAM1 [Strigops habroptila]
SPAM1 [Strigops habroptila]
Gene ID:115605380

Gene
MANEA [Pogona vitticeps]
MANEA [Pogona vitticeps]
Gene ID:110074132

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000932808	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000932808

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2022)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000932808.3

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

Description

This variant, c.175_177dup, results in the insertion of 1 amino acid(s) of the GAMT protein (p.Ser59dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs768895098, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with GAMT-related conditions. ClinVar contains an entry for this variant (Variation ID: 640432). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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