SLC22A16

solute carrier family 22 member 16, the group of Solute carrier family 22

Basic information

Region (hg38): 6:110424686-110476641

Links

ENSG00000004809 ∙ NCBI:85413 ∙ OMIM:608276 ∙ HGNC:20302 ∙ Uniprot:Q86VW1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC22A16 gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A16 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			19	2	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	2

Variants in SLC22A16

This is a list of pathogenic ClinVar variants found in the SLC22A16 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-110424907-G-A		not specified	Likely benign (Apr 13, 2022)
6-110424938-T-C		not specified	Uncertain significance (Jun 24, 2022)
6-110424964-C-T		not specified	Uncertain significance (Nov 06, 2023)
6-110425056-A-C		not specified	Uncertain significance (Nov 02, 2023)
6-110431212-A-G		not specified	Uncertain significance (Oct 20, 2023)
6-110431214-G-A		not specified	Uncertain significance (Jan 02, 2024)
6-110431236-G-A		not specified	Uncertain significance (Sep 06, 2022)
6-110431238-C-A		not specified	Uncertain significance (Mar 11, 2022)
6-110431263-C-T		not specified	Uncertain significance (Aug 08, 2022)
6-110435910-C-T		not specified	Uncertain significance (Jun 29, 2022)
6-110435927-A-C		not specified	Uncertain significance (Sep 26, 2022)
6-110435929-C-T		not specified	Uncertain significance (Nov 21, 2022)
6-110438737-C-T			Benign (May 21, 2018)
6-110438809-C-G		not specified	Uncertain significance (Feb 15, 2023)
6-110442247-G-C		not specified	Uncertain significance (Dec 16, 2023)
6-110442258-T-C		not specified	Uncertain significance (Mar 01, 2023)
6-110442269-A-C		not specified	Uncertain significance (Jan 08, 2024)
6-110442289-A-G		not specified	Uncertain significance (Dec 19, 2022)
6-110442414-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-110442415-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-110442454-G-T		not specified	Uncertain significance (Apr 13, 2022)
6-110442495-A-G		not specified	Uncertain significance (Dec 27, 2023)
6-110442539-G-C			Benign (May 21, 2018)
6-110442569-C-G		not specified	Uncertain significance (Oct 26, 2021)
6-110442610-T-A		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A16	protein_coding	protein_coding	ENST00000368919	8	51955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.31e-27	0.00000345	125571	0	177	125748	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.636	347	315	1.10	0.0000166	3748
Missense in Polyphen		126	115.92	1.087		1397
Synonymous	-0.750	137	126	1.08	0.00000732	1152
Loss of Function	-1.94	34	23.8	1.43	0.00000120	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00155
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.00104	0.00104
Middle Eastern	0.000329	0.000326
South Asian	0.000329	0.000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High affinity carnitine transporter; the uptake is partially sodium-ion dependent. Thought to mediate the L-carnitine secretion mechanism from testis epididymal epithelium into the lumen which is involved in the maturation of spermatozoa. Also transports organic cations such as tetraethylammonium (TEA) and doxorubicin. The uptake of TEA is inhibited by various organic cations. The uptake of doxorubicin is sodium-independent. {ECO:0000269|PubMed:12089149, ECO:0000269|PubMed:15963465}.
• Pathway: Doxorubicin Pathway (Cancer Cell), Pharmacodynamics;Doxorubicin Pathway, Pharmacokinetics;Doxorubicin Metabolism Pathway;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Organic cation/anion/zwitterion transport (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.671
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.83

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.264

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a16

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;single fertilization;organic cation transport;amine transport;carnitine transport;cell differentiation;flagellated sperm motility;acid secretion;carnitine transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: amine transmembrane transporter activity;organic cation transmembrane transporter activity;carnitine transmembrane transporter activity