NM_003042.4(SLC6A1):c.131G>A (p.Arg44Gln) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 22, 2022
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:: RCV001092965.24

Allele description [Variation Report for NM_003042.4(SLC6A1):c.131G>A (p.Arg44Gln)]

NM_003042.4(SLC6A1):c.131G>A (p.Arg44Gln)

Genes:

SLC6A1-AS1:SLC6A1 antisense RNA 1 [Gene - HGNC]
SLC6A1:solute carrier family 6 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_003042.4(SLC6A1):c.131G>A (p.Arg44Gln)

HGVS:

NC_000003.12:g.11017342G>A
NG_053003.1:g.29614G>A
NM_001348250.2:c.131G>A
NM_001348251.2:c.-123+83G>A
NM_001348252.2:c.-165+83G>A
NM_001348253.2:c.-165+83G>A
NM_003042.4:c.131G>AMANE SELECT
NP_001335179.1:p.Arg44Gln
NP_003033.3:p.Arg44Gln
NC_000003.11:g.11059028G>A
NM_003042.3:c.131G>A
P30531:p.Arg44Gln

Protein change:

R44Q; ARG44GLN

Links:

UniProtKB: P30531#VAR_073852; OMIM: 137165.0001; dbSNP: rs794726859

NCBI 1000 Genomes Browser:

rs794726859

Molecular consequence:

NM_001348251.2:c.-123+83G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001348252.2:c.-165+83G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001348253.2:c.-165+83G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001348250.2:c.131G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003042.4:c.131G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV001249723	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Nov 1, 2019)	germline	clinical testing	Citation Link,
SCV002567446	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 22, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001249723

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Nov 1, 2019)

germline

clinical testing

Citation Link,

SCV002567446

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 22, 2022)

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	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001249723.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV002567446.2

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

Description

Reported in heterozygous state in one individual in an autism and intellectual disability cohort in published literature (Stessman et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29086036, 27959697, 25865495, 33004838, 35295842, 28191889)

#	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: Nov 24, 2024

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