SLC10A4

solute carrier family 10 member 4, the group of Solute carrier family 10

Basic information

Region (hg38): 4:48483342-48489526

Links

ENSG00000145248 ∙ NCBI:201780 ∙ OMIM:618563 ∙ HGNC:22980 ∙ Uniprot:Q96EP9 ∙ 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 SLC10A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC10A4 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in SLC10A4

This is a list of pathogenic ClinVar variants found in the SLC10A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-48483584-C-A		not specified	Uncertain significance (Dec 28, 2022)
4-48483595-G-T		not specified	Uncertain significance (Jan 26, 2022)
4-48483683-G-A		not specified	Uncertain significance (Oct 27, 2021)
4-48483694-G-C		not specified	Uncertain significance (Sep 14, 2021)
4-48483710-T-C		not specified	Uncertain significance (Jul 09, 2021)
4-48483710-T-G		not specified	Uncertain significance (Sep 16, 2021)
4-48483766-A-G		not specified	Uncertain significance (Aug 30, 2021)
4-48483845-C-A		not specified	Uncertain significance (Jun 04, 2024)
4-48483883-T-C		not specified	Uncertain significance (Aug 08, 2022)
4-48483958-G-A		not specified	Uncertain significance (Jan 04, 2022)
4-48483962-G-T		not specified	Uncertain significance (Feb 12, 2024)
4-48484033-G-A		not specified	Uncertain significance (Sep 22, 2023)
4-48484118-T-A		not specified	Uncertain significance (Jan 29, 2024)
4-48485050-G-A		not specified	Uncertain significance (Sep 14, 2022)
4-48485050-G-C		not specified	Uncertain significance (Nov 22, 2023)
4-48485105-G-A		not specified	Uncertain significance (Feb 23, 2023)
4-48485107-T-C		not specified	Uncertain significance (Dec 19, 2022)
4-48488478-G-A		not specified	Uncertain significance (Jan 03, 2022)
4-48488523-G-A		not specified	Uncertain significance (Jun 18, 2021)
4-48488565-T-A		not specified	Uncertain significance (Aug 13, 2021)
4-48488601-C-T		not specified	Uncertain significance (Jul 09, 2021)
4-48488659-C-T		not specified	Uncertain significance (Jan 03, 2024)
4-48488770-A-G		not specified	Uncertain significance (Nov 09, 2021)
4-48488781-G-A		not specified	Uncertain significance (Mar 31, 2024)
4-48488790-A-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC10A4	protein_coding	protein_coding	ENST00000273861	3	5854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0279	0.927	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.997	187	230	0.815	0.0000116	2790
Missense in Polyphen		70	89.114	0.78551		1038
Synonymous	1.06	89	103	0.867	0.00000576	977
Loss of Function	1.72	4	9.82	0.407	4.98e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000167	0.000163
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transporter for bile acids. {ECO:0000269|PubMed:23589386}.

Haploinsufficiency Scores

• pHI: 0.0416
• hipred: N
• hipred_score: 0.445
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0569

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc10a4
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: sodium ion transport;bile acid and bile salt transport;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: bile acid:sodium symporter activity