NM_001080397.3(SLC45A1):c.629C>T (p.Ala210Val) AND Intellectual developmental disorder with neuropsychiatric features

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jun 28, 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:: RCV000492063.5

Allele description [Variation Report for NM_001080397.3(SLC45A1):c.629C>T (p.Ala210Val)]

NM_001080397.3(SLC45A1):c.629C>T (p.Ala210Val)

Gene:

SLC45A1:solute carrier family 45 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.23

Genomic location:

Preferred name:

NM_001080397.3(SLC45A1):c.629C>T (p.Ala210Val)

Other names:

A210V

HGVS:

NC_000001.11:g.8325956C>T
NG_034025.1:g.12872C>T
NM_001080397.3:c.629C>TMANE SELECT
NM_001379614.1:c.629C>T
NM_001379615.1:c.536C>T
NM_001379616.1:c.536C>T
NM_001379617.1:c.23C>T
NM_001379618.1:c.23C>T
NP_001073866.3:p.Ala210Val
NP_001366543.1:p.Ala210Val
NP_001366544.1:p.Ala179Val
NP_001366545.1:p.Ala179Val
NP_001366546.1:p.Ala8Val
NP_001366547.1:p.Ala8Val
NC_000001.10:g.8386016C>T
NM_001080397.1:c.629C>T
NM_001080397.2:c.731C>T

Protein change:

A179V; ALA210VAL

Links:

OMIM: 605763.0001; dbSNP: rs150539474

NCBI 1000 Genomes Browser:

rs150539474

Molecular consequence:

NM_001080397.3:c.629C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379614.1:c.629C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379615.1:c.536C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379616.1:c.536C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379617.1:c.23C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379618.1:c.23C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Intellectual developmental disorder with neuropsychiatric features
Identifiers:: MONDO: MONDO:0044322; MedGen: C4479636; OMIM: 617532

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000580684	OMIM	no assertion criteria provided	Pathogenic (Jun 26, 2017)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002023567	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 28, 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

SCV000580684

OMIM

no assertion criteria provided

Pathogenic
(Jun 26, 2017)

germline

literature only

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

SCV002023567

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 28, 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
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Dysfunction of the Cerebral Glucose Transporter SLC45A1 in Individuals with Intellectual Disability and Epilepsy.

Srour M, Shimokawa N, Hamdan FF, Nassif C, Poulin C, Al Gazali L, Rosenfeld JA, Koibuchi N, Rouleau GA, Al Shamsi A, Michaud JL.

Am J Hum Genet. 2017 May 4;100(5):824-830. doi: 10.1016/j.ajhg.2017.03.009. Epub 2017 Apr 20.

PubMed [citation]

PMID:: 28434495
PMCID:: PMC5420346

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV000580684.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 2 sisters, born of consanguineous Palestinian parents, with intellectual developmental disorder with neuropsychiatric features (IDDNPF; 617532), Srour et al. (2017) identified a homozygous c.629C-T transition (c.629C-T, NM_001080397.1) in exon 3 of the SLC45A1 gene, resulting in an ala210-to-val (A210V) substitution at a conserved residue at the beginning of the intracellular loop just after the fourth transmembrane domain. The mutation, which was found by a combination of homozygosity mapping and whole-exome sequencing, was confirmed by Sanger sequencing and segregated with the disorder in the family. It was not found in 95 ethnically matched controls, but was present at a very low frequency in the ExAC database. In vitro functional expression studies in COS-7 cells showed that the glucose transport activity of the mutant protein was decreased by about 33% compared to controls.

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

From Revvity Omics, Revvity, SCV002023567.3

#	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: Mar 16, 2024

ClinVar

Relating variation to medicine