NM_000156.6(GAMT):c.181+7C>T AND Cerebral creatine deficiency syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (1 submission)
Last evaluated:: Feb 6, 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:: RCV002114821.5

Allele description

NM_000156.6(GAMT):c.181+7C>T

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.181+7C>T

HGVS:

NC_000019.10:g.1401289G>A
NG_009785.1:g.5265C>T
NM_000156.6:c.181+7C>TMANE SELECT
NM_138924.3:c.181+7C>T
NC_000019.9:g.1401288G>A

Links:

dbSNP: rs2144640848

NCBI 1000 Genomes Browser:

rs2144640848

Molecular consequence:

NM_000156.6:c.181+7C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_138924.3:c.181+7C>T - intron variant - [Sequence Ontology: SO:0001627]

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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lectin, mannose-binding 2-like a isoform X1 [Epinephelus fuscoguttatus]
lectin, mannose-binding 2-like a isoform X1 [Epinephelus fuscoguttatus]
gi|2276533945|ref|XP_049459407.1|

Protein
PREDICTED: Epinephelus fuscoguttatus lectin, mannose-binding 2-like a (lman2la),...
PREDICTED: Epinephelus fuscoguttatus lectin, mannose-binding 2-like a (lman2la), transcript variant X2, mRNA
gi|2276533946|ref|XM_049603451.1|

Nucleotide
ubiquitin carboxyl-terminal hydrolase BAP1 isoform X4 [Homo sapiens]
ubiquitin carboxyl-terminal hydrolase BAP1 isoform X4 [Homo sapiens]
gi|2462593017|ref|XP_054204033.1|

Protein
von Willebrand factor A domain-containing protein 5B2 isoform 1 [Homo sapiens]
von Willebrand factor A domain-containing protein 5B2 isoform 1 [Homo sapiens]
gi|1955886577|ref|NP_001377775.1|

Protein
Homo sapiens von Willebrand factor A domain containing 5B2 (VWA5B2), transcript ...
Homo sapiens von Willebrand factor A domain containing 5B2 (VWA5B2), transcript variant 9, mRNA
gi|1955886576|ref|NM_001390846.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002441213	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Feb 6, 2021)	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

SCV002441213

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Feb 6, 2021)

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 Invitae, SCV002441213.3

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

#	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: Feb 28, 2024

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