SLC36A3

solute carrier family 36 member 3, the group of Solute carrier family 36

Basic information

Region (hg38): 5:151276358-151303766

Links

ENSG00000186334 ∙ NCBI:285641 ∙ OMIM:608332 ∙ HGNC:19659 ∙ Uniprot:Q495N2 ∙ 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 SLC36A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC36A3 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						0
missense			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in SLC36A3

This is a list of pathogenic ClinVar variants found in the SLC36A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151277428-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-151277505-A-G		not specified	Uncertain significance (Dec 01, 2022)
5-151277520-A-G		not specified	Uncertain significance (Jun 18, 2024)
5-151277527-C-T		not specified	Uncertain significance (Aug 05, 2023)
5-151277580-A-T		not specified	Uncertain significance (Jul 13, 2021)
5-151277605-C-T		not specified	Uncertain significance (Oct 04, 2022)
5-151277638-G-A		not specified	Uncertain significance (Jan 07, 2022)
5-151281037-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-151281038-G-A		not specified	Uncertain significance (May 16, 2022)
5-151281094-G-A		not specified	Uncertain significance (Aug 14, 2023)
5-151281136-G-C		not specified	Uncertain significance (Apr 29, 2024)
5-151281149-C-T		not specified	Uncertain significance (Jan 18, 2022)
5-151281174-C-G		not specified	Uncertain significance (Jan 23, 2024)
5-151284048-A-G		not specified	Uncertain significance (Jun 26, 2023)
5-151284645-T-C		not specified	Uncertain significance (Jul 14, 2021)
5-151284678-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-151284682-C-A		not specified	Uncertain significance (Jun 22, 2024)
5-151287274-A-G		not specified	Uncertain significance (Sep 27, 2021)
5-151287290-T-C		not specified	Uncertain significance (Nov 09, 2021)
5-151287307-G-A		not specified	Uncertain significance (May 25, 2022)
5-151287323-C-G		not specified	Uncertain significance (Jan 17, 2024)
5-151287345-C-A		not specified	Uncertain significance (Nov 29, 2023)
5-151287390-G-T		not specified	Uncertain significance (Apr 07, 2023)
5-151287413-G-T		not specified	Uncertain significance (Jan 18, 2022)
5-151287446-C-T		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC36A3	protein_coding	protein_coding	ENST00000377713	11	27005

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00203	0.994	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0858	264	260	1.01	0.0000134	3319
Missense in Polyphen		51	55.675	0.91603		702
Synonymous	0.809	97	108	0.901	0.00000617	1022
Loss of Function	2.52	8	20.3	0.395	9.53e-7	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00160	0.00158
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000634	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000503	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.57

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.147

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc36a3

Gene ontology

• Biological process: amino acid transmembrane transport;L-alanine transport;glycine transport;proline transmembrane transport;proton transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: amino acid:proton symporter activity;proton transmembrane transporter activity;amino acid transmembrane transporter activity;L-alanine transmembrane transporter activity;glycine transmembrane transporter activity;L-proline transmembrane transporter activity