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NM_003060.4(SLC22A5):c.-149G>A AND SLC22A5-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 1, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003407353.5

Allele description [Variation Report for NM_003060.4(SLC22A5):c.-149G>A]

NM_003060.4(SLC22A5):c.-149G>A

Genes:
LOC129994569:ATAC-STARR-seq lymphoblastoid silent region 16317 [Gene]
MIR3936HG:MIR3936 host gene [Gene - HGNC]
SLC22A5:solute carrier family 22 member 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.1
Genomic location:
Preferred name:
NM_003060.4(SLC22A5):c.-149G>A
HGVS:
  • NC_000005.10:g.132369824G>A
  • NG_008982.2:g.5121G>A
  • NG_174015.1:g.332G>A
  • NM_001308122.2:c.-149G>A
  • NM_003060.4:c.-149G>AMANE SELECT
  • NC_000005.9:g.131705516G>A
  • NM_003060.3:c.-149G>A
Nucleotide change:
-149G-A
Links:
OMIM: 603377.0023; dbSNP: rs57262206
NCBI 1000 Genomes Browser:
rs57262206
Molecular consequence:
  • NM_001308122.2:c.-149G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_003060.4:c.-149G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:
SLC22A5-related disorder
Synonyms:
SLC22A5-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004114924PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jul 1, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004114924.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The SLC22A5 c.-149G>A variant is located in the 5' untranslated region. This variant has been reported, in the homozygous or compound heterozygous state, in numerous individuals with primary carnitine deficiency (PCD) (Ferdinandusse et al. 2019. PubMed ID: 31187905; Verbeeten et al. 2020. PubMed ID: 31864849). It was found in in the homozygous and apparently compound heterozogous state in several individuals who were classified as having a likely benign form of PCD who were asymptomatic or only had mild symptoms, regardless of treatment. (Crefcoeur et al. 2023. PubMed ID: 37487700). The c.-149G>A variant was predicted to create a novel translation initiation codon upstream of the canonical AUG start codon, and in a functional assay using a luciferase reporter construct, the c.-149G>A variant was found to reduce luciferase activity to 11% of control (Ferdinandusse et al. 2019. PubMed ID: 31187905). Furthermore, carnitine transport activity was reduced in patient fibroblasts with the c.-149G>A variant (Ferdinandusse et al. 2019. PubMed ID: 31187905; Verbeeten et al. 2020. PubMed ID: 31864849). Based on these observations, we classify this variant as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024