NM_000156.6(GAMT):c.59G>C (p.Trp20Ser) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 3, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000986201.4

Allele description [Variation Report for NM_000156.6(GAMT):c.59G>C (p.Trp20Ser)]

NM_000156.6(GAMT):c.59G>C (p.Trp20Ser)

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.59G>C (p.Trp20Ser)

Other names:

NM_000156.6(GAMT):c.59G>C

HGVS:

NC_000019.10:g.1401418C>G
NG_009785.1:g.5136G>C
NM_000156.6:c.59G>CMANE SELECT
NM_138924.3:c.59G>C
NP_000147.1:p.Trp20Ser
NP_620279.1:p.Trp20Ser
NC_000019.9:g.1401417C>G
NM_000156.4:c.59G>C
NM_000156.5:c.59G>C
Q14353:p.Trp20Ser

Protein change:

W20S; TRP20SER

Links:

UniProtKB: Q14353#VAR_058102; OMIM: 601240.0003; dbSNP: rs80338734

NCBI 1000 Genomes Browser:

rs80338734

Molecular consequence:

NM_000156.6:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_138924.3:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001135124	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Pathogenic (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001777342	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 3, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001135124

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Pathogenic
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV001777342

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 3, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Mendelics, SCV001135124.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001777342.2

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

Description

Pathogenic founder variant in Portuguese population with a carrier frequency of 0.8% (Mercimek-Mahmutoglu et al. 2006); Published functional studies demonstrate that introduction of GAMT-W20S contructs into HeLa cells was associated with no increase of GAMT activity whereas the wild type protein resulted in increased activity (Almeida et al., 2007); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28808834, 28055022, 19892372, 24268530, 21140503, 17336114, 15108290, 23031365, 19027335, 26003046, 16899382, 16855203, 15651030, 31589614)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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