NM_003060.4(SLC22A5):c.1053-3_1053-2delinsTC AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 31, 2016
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:: RCV000378290.1

Allele description [Variation Report for NM_003060.4(SLC22A5):c.1053-3_1053-2delinsTC]

NM_003060.4(SLC22A5):c.1053-3_1053-2delinsTC

Gene:

SLC22A5:solute carrier family 22 member 5 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

5q31.1

Genomic location:

Preferred name:

NM_003060.4(SLC22A5):c.1053-3_1053-2delinsTC

HGVS:

NC_000005.10:g.132390687_132390688delinsTC
NG_008982.2:g.25984_25985delinsTC
NM_001308122.2:c.1125-3_1125-2delinsTC
NM_003060.4:c.1053-3_1053-2delinsTCMANE SELECT
NC_000005.9:g.131726379_131726380delinsTC
NM_003060.3:c.1053-3_1053-2delCAinsTC

Links:

dbSNP: rs886041967

NCBI 1000 Genomes Browser:

rs886041967

Molecular consequence:

NM_001308122.2:c.1125-3_1125-2delinsTC - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_003060.4:c.1053-3_1053-2delinsTC - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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zinc finger, imprinted 1 isoform X1 [Mus musculus]
zinc finger, imprinted 1 isoform X1 [Mus musculus]
gi|755519334|ref|XP_011248797.1|

Protein
Mus musculus
Mus musculus
Genetic and epigenetic determinants of neurogenesis and myogenesis [ChIP-seq]

BioProject
PRDM1 PR/SET domain 1 [Sus scrofa]
PRDM1 PR/SET domain 1 [Sus scrofa]
Gene ID:100154284

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000330779	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 31, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330779

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 31, 2016)

germline

clinical testing

Citation Link

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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

Details of each submission

From GeneDx, SCV000330779.6

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

Description

The c.1053-3_1053-2delCAinsTC variant in the SLC22A5 gene destroys the canonical splice acceptor site in intron 6. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.1053-3_1053-2delCAinsTC variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.1053-3_1053-2delCAinsTC to be a pathogenic variant.

#	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: Apr 23, 2022

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