SLC6A18

solute carrier family 6 member 18, the group of Solute carrier family 6

Basic information

Region (hg38): 5:1225380-1246189

Links

ENSG00000164363 ∙ NCBI:348932 ∙ OMIM:610300 ∙ HGNC:26441 ∙ Uniprot:Q96N87 ∙ 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 SLC6A18 gene.

• Inborn genetic diseases (45 variants)
• not provided (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A18 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	5	7
missense			39	7	8	54
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	39	9	14

Variants in SLC6A18

This is a list of pathogenic ClinVar variants found in the SLC6A18 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-1225509-C-T		not specified	Likely benign (Dec 01, 2022)
5-1225532-C-T		not specified	Uncertain significance (Jul 11, 2022)
5-1225604-C-T		not specified	Uncertain significance (Nov 18, 2022)
5-1225619-T-C		not specified	Uncertain significance (Feb 02, 2022)
5-1232239-G-A		not specified	Uncertain significance (Dec 17, 2023)
5-1232257-G-A		not specified	Uncertain significance (Sep 27, 2021)
5-1232278-G-A		not specified	Likely benign (Dec 17, 2023)
5-1232305-C-T		not specified	Uncertain significance (Aug 28, 2023)
5-1232323-G-A		not specified	Uncertain significance (Feb 21, 2024)
5-1232329-A-T		not specified	Uncertain significance (Feb 07, 2023)
5-1232330-C-T			Benign (Mar 29, 2018)
5-1232751-G-C		not specified	Uncertain significance (Jan 03, 2024)
5-1232787-T-A		not specified	Uncertain significance (Dec 28, 2023)
5-1232873-G-A		not specified	Uncertain significance (Aug 08, 2022)
5-1235481-G-A		not specified	Uncertain significance (Dec 16, 2023)
5-1235512-C-T			Benign (Feb 26, 2018)
5-1235513-G-A		not specified	Uncertain significance (Jan 30, 2024)
5-1235531-C-T		not specified	Uncertain significance (Jan 10, 2023)
5-1235546-A-T		not specified	Uncertain significance (Jan 19, 2024)
5-1235576-A-G		not specified	Likely benign (May 03, 2023)
5-1235621-G-A		not specified	Uncertain significance (Dec 14, 2021)
5-1235629-G-A			Likely benign (Dec 01, 2022)
5-1238000-C-T			Benign (Mar 29, 2018)
5-1239471-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-1239472-G-A		not specified	Likely benign (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A18	protein_coding	protein_coding	ENST00000324642	12	20835

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.80e-22	0.000445	51499	16859	57390	125748	0.360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.194	395	406	0.973	0.0000262	4034
Missense in Polyphen		157	149.04	1.0534		1697
Synonymous	0.526	182	191	0.952	0.0000142	1293
Loss of Function	-0.425	31	28.6	1.09	0.00000142	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.725	0.722
Ashkenazi Jewish	0.295	0.293
East Asian	0.238	0.238
Finnish	0.325	0.325
European (Non-Finnish)	0.387	0.385
Middle Eastern	0.238	0.238
South Asian	0.402	0.396
Other	0.351	0.347

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a sodium and chloride-dependent neutral amino acid transporter. {ECO:0000250}.
• Disease: DISEASE: Note=Genetic variations in SLC6A18 might contribute to the disease phentotype in some individuals with iminoglycinuria or hyperglycinuria, that carry variants in SLC36A2, SLC6A19 or SLC6A20 (PubMed:19033659). {ECO:0000269|PubMed:19033659}.
• 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: 0.107

Intolerance Scores

• loftool: 0.847
• rvis_EVS: 1.01
• rvis_percentile_EVS: 90.81

Haploinsufficiency Scores

• pHI: 0.0550
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.377

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a18
• Phenotype: homeostasis/metabolism 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); renal/urinary system phenotype

Gene ontology

• Biological process: amino acid transmembrane transport;neurotransmitter transport;amino acid transport;neutral amino acid transport
• Cellular component: plasma membrane;integral component of plasma membrane;apical plasma membrane;brush border membrane
• Molecular function: neurotransmitter:sodium symporter activity;amino acid transmembrane transporter activity;neutral amino acid transmembrane transporter activity