NM_003060.4(SLC22A5):c.1195del (p.Arg399fs) AND Renal carnitine transport defect

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 12, 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:: RCV002307263.2

Allele description [Variation Report for NM_003060.4(SLC22A5):c.1195del (p.Arg399fs)]

NM_003060.4(SLC22A5):c.1195del (p.Arg399fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

5q31.1

Genomic location:

Preferred name:

NM_003060.4(SLC22A5):c.1195del (p.Arg399fs)

HGVS:

NC_000005.10:g.132390832del
NG_008982.2:g.26129del
NM_001308122.2:c.1267del
NM_003060.4:c.1195delMANE SELECT
NP_001295051.1:p.Arg423fs
NP_003051.1:p.Arg399fs
NC_000005.9:g.131726524del

Protein change:

R399fs

Molecular consequence:

NM_001308122.2:c.1267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003060.4:c.1195del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Renal carnitine transport defect (CDSP)
Synonyms:: CARNITINE TRANSPORTER, PLASMA-MEMBRANE, DEFICIENCY OF; Primary carnitine deficiency; Carnitine uptake defect; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008919; MedGen: C0342788; Orphanet: 158; OMIM: 212140

Recent activity

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4933432I09Rik RIKEN cDNA 4933432I09 gene [Mus musculus]
4933432I09Rik RIKEN cDNA 4933432I09 gene [Mus musculus]
Gene ID:66779

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002604734	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Dec 12, 2021)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002604734

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Dec 12, 2021)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Myriad Genetics, Inc., SCV002604734.2

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

Description

NM_003060.3(SLC22A5):c.1195delC(R399Gfs*34) is expected to be pathogenic in the context of primary carnitine deficiency. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in SLC22A5, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

#	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

Last Updated: Dec 24, 2022

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