SLC10A3

protein-coding

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

Gene summary

This gene maps to a GC-rich region of the X chromosome and was identified by its proximity to a CpG island. It is thought to be a housekeeping gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Dec 2008]

MANE transcript

NM_019848.5

Inheritance

—

ClinVar variants

U:65B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:154,487,306-154,490,690

External References & Databases

Ensembl (ENSG00000126903)

Transcript & Mutation Effects

hg38 • Region Span ~3.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC10A3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019848.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	3 clinvar	1 clinvar	11
missense			56 clinvar	6 clinvar		62
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	65	9	1	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019848.5	RefSeq	NP_062822.1	1	MANE Select
ENST00000651600.1	Ensembl	ENSP00000499188.1	1	MANE Select
NM_001142391.3	RefSeq	NP_001135863.1	2	Standard
NM_001142392.3	RefSeq	NP_001135864.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to retinoic acid
transmembrane transport

Molecular Function

symporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263512
Coding exons: 1
Length: 3372
Individuals with no LoFs: 125686
Homozygous LoFs: 4
Heterozygous LoFs: 6
Defined: 125696
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.22	159	208	0.763	0.0000173	3048
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000073	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.000061	0.000044	rare
South Asian	0.000052	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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