NM_000156.6(GAMT):c.432_433dup (p.His145fs) AND Cerebral creatine deficiency syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 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:: RCV001883192.3

Allele description [Variation Report for NM_000156.6(GAMT):c.432_433dup (p.His145fs)]

NM_000156.6(GAMT):c.432_433dup (p.His145fs)

Gene:

GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_000156.6(GAMT):c.432_433dup (p.His145fs)

HGVS:

NC_000019.10:g.1399154_1399155dup
NG_009785.1:g.7399_7400dup
NM_000156.6:c.432_433dupMANE SELECT
NM_138924.3:c.432_433dup
NP_000147.1:p.His145fs
NP_620279.1:p.His145fs
NC_000019.9:g.1399152_1399153insGC
NC_000019.9:g.1399153_1399154dup

Protein change:

H145fs

Links:

dbSNP: rs2144636785

NCBI 1000 Genomes Browser:

rs2144636785

Molecular consequence:

NM_000156.6:c.432_433dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_138924.3:c.432_433dup - frameshift variant - [Sequence Ontology: SO:0001589]

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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synaptojanin-1 isoform X23 [Mus musculus]
synaptojanin-1 isoform X23 [Mus musculus]
gi|1039750357|ref|XP_017172326.1|

Protein
RefSeq RNA Links for Gene (Select 320910) (2)
Nucleotide
Profile neighbors for GEO Profiles (Select 16488347) (200)
GEO Profiles
Related DataSets for GEO Profiles (Select 18105007) (1)
GEO DataSets
Self-renewing memory B cell
Self-renewing memory B cell
Accession: GDS1695

GEO DataSets

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002145177	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 1, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15108290, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002145177

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 1, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Characterization of seven novel mutations in seven patients with GAMT deficiency.

Item CB, Mercimek-Mahmutoglu S, Battini R, Edlinger-Horvat C, Stromberger C, Bodamer O, Mühl A, Vilaseca MA, Korall H, Stöckler-Ipsiroglu S.

Hum Mutat. 2004 May;23(5):524.

PubMed [citation]

PMID:: 15108290

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, SCV002145177.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with GAMT-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.His145Argfs*17) in the GAMT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GAMT are known to be pathogenic (PMID: 15108290).

#	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 20, 2024

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