SLC22A5

solute carrier family 22 member 5, the group of Solute carrier family 22

Basic information

Region (hg38): 5:132369710-132395613

Previous symbols: [ "CDSP" ]

Links

ENSG00000197375

∙ NCBI:6584 ∙ OMIM:603377 ∙ HGNC:10969 ∙ Uniprot:O76082 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

systemic primary carnitine deficiency disease (Definitive), mode of inheritance: AR
systemic primary carnitine deficiency disease (Definitive), mode of inheritance: AR
systemic primary carnitine deficiency disease (Strong), mode of inheritance: AR
systemic primary carnitine deficiency disease (Strong), mode of inheritance: AR
systemic primary carnitine deficiency disease (Supportive), mode of inheritance: AR
systemic primary carnitine deficiency disease (Definitive), mode of inheritance: AR
systemic primary carnitine deficiency disease (Definitive), mode of inheritance: AR
short QT syndrome (Disputed Evidence), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Carnitine deficiency, systemic primary	AR	Biochemical; Pharmacogenomic	Early disease recognition with prompt carnitine therapy can be immediately life-saving and beneficial long-term; Certain agents (eg, specific antibiotics) have been reported to precipitate severe reactions, and should be avoided	Biochemical; Cardiovascular; Gastrointestinal; Musculoskeletal; Neurologic	234182; 7432384; 7254270; 7131143; 3974805; 3181209; 3185635; 2235122; 1763895; 2235122; 9826541; 9700603; 11261427; 9634512; 9916797; 11715001; 12210323; 15303004; 16652335; 17126586; 20027113; 20574985; 21922592; 22566287; 22989098; 23379544

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC22A5 gene.

Renal_carnitine_transport_defect (1119 variants)
not_provided (180 variants)
Decreased_circulating_carnitine_concentration (94 variants)
not_specified (63 variants)
Inborn_genetic_diseases (46 variants)
Carnitine_deficiency (43 variants)
SLC22A5-related_disorder (27 variants)
See_cases (2 variants)
High_myopia (1 variants)
Abnormality_of_the_nervous_system (1 variants)
Dilated_cardiomyopathy_1A (1 variants)
Congenital_myasthenic_syndrome_20 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003060.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	8 clinvar	290 clinvar	2 clinvar	301
missense	19 clinvar	117 clinvar	373 clinvar	29 clinvar		538
nonsense	29 clinvar	17 clinvar	2 clinvar			48
start loss	2	4				6
frameshift	40 clinvar	36 clinvar	1 clinvar			77
splice donor/acceptor (+/-2bp)	10 clinvar	26 clinvar				36
Total	100	201	384	319	2

Highest pathogenic variant AF is 0.0026605164

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A5	protein_coding	protein_coding	ENST00000245407	10	25863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-16	0.0133	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.357	332	314	1.06	0.0000173	3591
Missense in Polyphen		79	78.584	1.0053		889
Synonymous	-0.847	144	132	1.09	0.00000752	1180
Loss of Function	0.160	24	24.9	0.965	0.00000135	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000723	0.000724
Ashkenazi Jewish	0.00	0.00
East Asian	0.00169	0.00169
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000318	0.000316
Middle Eastern	0.00169	0.00169
South Asian	0.000395	0.000392
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Sodium-ion dependent, high affinity carnitine transporter. Involved in the active cellular uptake of carnitine. Transports one sodium ion with one molecule of carnitine. Also transports organic cations such as tetraethylammonium (TEA) without the involvement of sodium. Also relative uptake activity ratio of carnitine to TEA is 11.3. {ECO:0000269|PubMed:10454528}.;
Pathway: Choline metabolism in cancer - Homo sapiens (human);Metabolism of lipids;Import of palmitoyl-CoA into the mitochondrial matrix;Metabolism;Fatty acid metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Lipoate metabolism;Organic cation/anion/zwitterion transport;Glycerophospholipid metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

pRec: 0.286

Intolerance Scores

loftool: 0.403
rvis_EVS: 0.8
rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

pHI: 0.176
hipred: N
hipred_score: 0.224
ghis: 0.439

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.255

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Slc22a5
Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; renal/urinary system phenotype;

Zebrafish Information Network

Gene name: slc22a5
Affected structure: nucleate erythrocyte
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: sodium ion transport;drug transmembrane transport;quaternary ammonium group transport;carnitine transport;drug transport;quorum sensing involved in interaction with host;positive regulation of intestinal epithelial structure maintenance;sodium-dependent organic cation transport;carnitine transmembrane transport
Cellular component: plasma membrane;integral component of membrane;apical plasma membrane;brush border membrane;extracellular exosome
Molecular function: protein binding;ATP binding;carnitine transmembrane transporter activity;drug transmembrane transporter activity;symporter activity;quaternary ammonium group transmembrane transporter activity;PDZ domain binding