NM_003060.4(SLC22A5):c.592G>T (p.Val198Leu) AND Renal carnitine transport defect

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 3, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000781949.4

Allele description [Variation Report for NM_003060.4(SLC22A5):c.592G>T (p.Val198Leu)]

NM_003060.4(SLC22A5):c.592G>T (p.Val198Leu)

Gene:

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.592G>T (p.Val198Leu)

Other names:

p.Val198Leu

HGVS:

NC_000005.10:g.132384241G>T
NG_008982.2:g.19538G>T
NM_001308122.2:c.664G>T
NM_003060.4:c.592G>TMANE SELECT
NP_001295051.1:p.Val222Leu
NP_001295051.1:p.Val222Leu
NP_003051.1:p.Val198Leu
NC_000005.9:g.131719933G>T
NM_001308122.1:c.664G>T

Protein change:

V198L

Links:

dbSNP: rs757979350

NCBI 1000 Genomes Browser:

rs757979350

Molecular consequence:

NM_001308122.2:c.664G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003060.4:c.592G>T - missense variant - [Sequence Ontology: SO:0001583]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000920393	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 2, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002576593	Giacomini Lab, University of California, San Francisco	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 3, 2022)	germline, not applicable	research, in vitro	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000920393

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 2, 2019)

germline

clinical testing

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

SCV002576593

Giacomini Lab, University of California, San Francisco

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Oct 3, 2022)

germline, not applicable

research, in vitro

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	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	in vitro
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

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 Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital, SCV000920393.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Giacomini Lab, University of California, San Francisco, SCV002576593.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)
2	not provided	not provided	not provided	not provided	in vitro	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
2	not applicable	not applicable	not provided	not provided	assert pathogenicity		not provided	not provided	not provided	not provided

Last Updated: Feb 4, 2024

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