SLC22A25

protein-coding

solute carrier family 22 member 25, the group of Solute carrier family 22

Gene summary

Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_199352.6

Inheritance

—

ClinVar variants

U:83B:22

Top phenotype

SLC22A25-related disorder

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr11:63,158,437-63,243,599

External References & Databases

Ensembl (ENSG00000196600)

Transcript & Mutation Effects

hg38 • Region Span ~85.2 kb

Loading mutation effect viewer...

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 SLC22A25 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 92

SLC22A25-related disorderTotal: 10

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199352.6. 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			1 clinvar	5 clinvar		6
missense			82 clinvar	15 clinvar		97
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	83	21	1	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199352.6	RefSeq	NP_955384.3	9	MANE Select
ENST00000306494.11	Ensembl	ENSP00000307443.6	9	MANE Select
NM_001394058.1	RefSeq	NP_001380987.1	7	Standard
NM_001394059.1	RefSeq	NP_001380988.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transmembrane transport

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306494
Coding exons: 9
Length: 65877
Individuals with no LoFs: 120825
Homozygous LoFs: 363
Heterozygous LoFs: 4555
Defined: 125743
p: 0.0198

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.44	372	302	1.23	0.0000151	3577
Missense (PolyPhen)		78	69.03	1.1299		882
Synonymous	-1.44	127	108	1.18	0.00000502	1119
Loss of Function	-0.493	23	20.6	1.12	0.00000101	224

Population LoF Frequency

Population	CAF	p-value	Status
African	0.24	0.20	notable
Latino/Admixed American	0.014	0.013	notable
Ashkenazi Jewish	0.012	0.0092	notable
East Asian	0.0012	0.0012	notable
Finnish	0.0060	0.0060	notable
European (Non-Finnish)	0.010	0.0096	notable
South Asian	0.0040	0.0037	notable
Other	0.019	0.015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.937
RVIS EVS: 0.69
RVIS percentile EVS: 85.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0472

Gene Damage Prediction

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