SLC10A3

solute carrier family 10 member 3, the group of Solute carrier family 10

Basic information

Region (hg38): X:154487306-154490690

Links

ENSG00000126903 ∙ NCBI:8273 ∙ OMIM:312090 ∙ HGNC:22979 ∙ Uniprot:P09131 ∙ 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 SLC10A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC10A3 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	2
missense			23	5		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	6	1

Variants in SLC10A3

This is a list of pathogenic ClinVar variants found in the SLC10A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154487610-T-C		not specified	Uncertain significance (May 01, 2024)
X-154487628-C-T		not specified	Uncertain significance (Aug 12, 2024)
X-154487629-G-A		not specified	Uncertain significance (Nov 17, 2022)
X-154487703-T-C		not specified	Uncertain significance (Mar 05, 2025)
X-154487707-C-T		not specified	Uncertain significance (Sep 29, 2023)
X-154487745-A-G		not specified	Uncertain significance (Mar 16, 2022)
X-154487773-T-C		not specified	Uncertain significance (Jul 20, 2021)
X-154487805-G-A		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
X-154487823-A-G		not specified	Uncertain significance (Sep 14, 2022)
X-154487827-G-C		not specified	Uncertain significance (Jan 24, 2025)
X-154487845-C-T		not specified	Uncertain significance (Mar 30, 2024)
X-154487846-G-A			Benign (Dec 14, 2017)
X-154487989-C-T		not specified	Uncertain significance (Mar 10, 2025)
X-154487998-T-C		not specified	Uncertain significance (Jan 24, 2025)
X-154488019-G-A		not specified	Uncertain significance (May 11, 2022)
X-154488033-G-A		not specified	Uncertain significance (Oct 19, 2024)
X-154488101-G-C		not specified	Uncertain significance (Mar 07, 2025)
X-154488194-C-T		not specified	Uncertain significance (Feb 13, 2024)
X-154488397-C-T		not specified	Likely benign (Mar 21, 2022)
X-154488400-T-C		not specified	Likely benign (Apr 18, 2023)
X-154488417-T-C		not specified	Uncertain significance (Mar 05, 2024)
X-154488453-C-T		not specified	Uncertain significance (Jan 31, 2022)
X-154488472-G-C		not specified	Uncertain significance (Nov 24, 2024)
X-154488487-C-T		not specified	Uncertain significance (Dec 21, 2023)
X-154488562-C-T		not specified	Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC10A3	protein_coding	protein_coding	ENST00000263512	1	3372

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.807	0.188	125686	4	6	125696	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	159	208	0.763	0.0000173	3048
Missense in Polyphen		44	79.889	0.55076		1305
Synonymous	-0.968	116	103	1.12	0.00000930	1120
Loss of Function	2.16	0	5.44	0.00	3.45e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000730	0.0000730
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000725	0.0000544
Finnish	0.0000629	0.0000462
European (Non-Finnish)	0.0000615	0.0000440
Middle Eastern	0.0000725	0.0000544
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The ubiquitous expression and the conservation of the sequence in distant animal species suggest that the gene codes for a protein with housekeeping functions.

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.261
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.277
• hipred: N
• hipred_score: 0.399
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc10a3

Gene ontology

• Biological process: response to retinoic acid;transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: symporter activity