SLC6A15

solute carrier family 6 member 15, the group of Solute carrier family 6

Basic information

Region (hg38): 12:84859491-84913629

Links

ENSG00000072041 ∙ NCBI:55117 ∙ OMIM:607971 ∙ HGNC:13621 ∙ Uniprot:Q9H2J7 ∙ 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 SLC6A15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A15 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					2	2
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	33	1	2

Variants in SLC6A15

This is a list of pathogenic ClinVar variants found in the SLC6A15 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-84861639-T-A		not specified	Uncertain significance (Jul 31, 2024)
12-84861658-G-A		not specified	Uncertain significance (Feb 15, 2025)
12-84861660-A-G		not specified	Uncertain significance (Dec 27, 2023)
12-84861684-A-G		not specified	Uncertain significance (Jul 16, 2024)
12-84861714-A-G		not specified	Uncertain significance (Feb 01, 2025)
12-84861717-G-A		not specified	Uncertain significance (Apr 07, 2022)
12-84861776-G-T		not specified	Uncertain significance (Sep 21, 2023)
12-84861813-C-T		not specified	Uncertain significance (Jul 16, 2024)
12-84861828-G-C		not specified	Uncertain significance (Nov 30, 2022)
12-84861861-A-G		not specified	Uncertain significance (Nov 15, 2024)
12-84861894-A-T		not specified	Uncertain significance (Aug 13, 2021)
12-84861906-C-T		not specified	Uncertain significance (Oct 25, 2023)
12-84861913-T-G		not specified	Uncertain significance (Jan 03, 2025)
12-84863542-A-G		not specified	Uncertain significance (Apr 06, 2024)
12-84863573-C-T		not specified	Uncertain significance (Aug 19, 2024)
12-84863589-G-A			Benign (Jun 26, 2018)
12-84863593-T-C		not specified	Uncertain significance (Jan 23, 2024)
12-84867035-T-C		not specified	Uncertain significance (May 14, 2024)
12-84867064-A-G		not specified	Uncertain significance (Feb 03, 2023)
12-84867122-T-A		not specified	Uncertain significance (Jul 20, 2021)
12-84867158-T-A		not specified	Uncertain significance (Feb 07, 2025)
12-84867167-T-A		not specified	Uncertain significance (Jan 18, 2025)
12-84870610-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-84870627-G-A		not specified	Uncertain significance (Aug 30, 2021)
12-84870633-G-A		not specified	Uncertain significance (Apr 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A15	protein_coding	protein_coding	ENST00000266682	11	53903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000604	0.999	125719	0	27	125746	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	284	386	0.737	0.0000188	4799
Missense in Polyphen		102	171.34	0.5953		2159
Synonymous	-0.171	140	137	1.02	0.00000702	1402
Loss of Function	3.24	11	30.2	0.364	0.00000151	391

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000200	0.000196
Other	0.000490	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a sodium-dependent neutral amino acid transporter. Exhibits preference for the branched-chain amino acids, particularly leucine, valine and isoleucine and methionine. Mediates the saturable, pH-sensitive and electrogenic cotransport of proline and sodium ions with a stoichiometry of 1:1. May have a role as transporter for neurotransmitter precursors into neurons. In contrast to other members of the neurotransmitter transporter family, does not appear to be chloride-dependent. {ECO:0000269|PubMed:16226721}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Amine compound SLC transporters;Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Na+/Cl- dependent neurotransmitter transporters (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.740
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.04

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.605
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a15
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: amino acid transmembrane transport;sodium ion transport;neurotransmitter transport;amino acid transport;neutral amino acid transport;leucine transport;proline transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: proline:sodium symporter activity;neurotransmitter transporter activity;neurotransmitter:sodium symporter activity;amino acid transmembrane transporter activity