SLCO6A1

protein-coding

solute carrier organic anion transporter family member 6A1, the group of Solute carrier organic anion transporter family

Gene summary

Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in sperm principal piece. Predicted to be part of CatSper complex. Predicted to be active in basolateral plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173488.5

Inheritance

—

ClinVar variants

U:79B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr5:102,371,774-102,499,016

External References & Databases

Ensembl (ENSG00000205359)

Transcript & Mutation Effects

hg38 • Region Span ~127.2 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 SLCO6A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173488.5. 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				2 clinvar	3 clinvar	5
missense			79 clinvar	9 clinvar	1 clinvar	89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	11	4	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173488.5	RefSeq	NP_775759.3	13	MANE Select
ENST00000506729.6	Ensembl	ENSP00000421339.1	13	MANE Select
NM_001289002.2	RefSeq	NP_001275931.1	13	Standard
NM_001289004.2	RefSeq	NP_001275933.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

sodium-independent organic anion transport
transmembrane transport

Molecular Function

sodium-independent organic anion transmembrane transporter activity

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000506729
Coding exons: 13
Length: 127235
Individuals with no LoFs: 125676
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125687
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.511	355	383	0.926	0.0000203	4629
Missense (PolyPhen)		96	108.88	0.88171		1411
Synonymous	0.356	130	135	0.961	0.00000731	1406
Loss of Function	1.55	21	30.2	0.696	0.00000135	447

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.000065	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000028	0.000026	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.721

Intolerance Scores

LoFtool: 0.664
RVIS EVS: 1.31
RVIS percentile EVS: 94.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0421

Gene Damage Prediction

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