SLCO2A1

solute carrier organic anion transporter family member 2A1, the group of Solute carrier organic anion transporter family

Basic information

Region (hg38): 3:133932701-134052184

Previous symbols: [ "SLC21A2", "MATR1" ]

Links

ENSG00000174640 ∙ NCBI:6578 ∙ OMIM:601460 ∙ HGNC:10955 ∙ Uniprot:Q92959 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypertrophic osteoarthropathy, primary, autosomal recessive, 2 (Strong), mode of inheritance: AR
• hypertrophic osteoarthropathy, primary, autosomal recessive, 2 (Definitive), mode of inheritance: AR
• pachydermoperiostosis (Supportive), mode of inheritance: AR
• chronic enteropathy associated with SLCO2A1 gene (Supportive), mode of inheritance: AR
• hypertrophic osteoarthropathy, primary, autosomal dominant (Definitive), mode of inheritance: AD
• hypertrophic osteoarthropathy, primary, autosomal recessive, 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypertrophic osteoarthropathy, primary, autosomal dominant; PHOAR2-enteropathy syndrome	AD/AR	Musculoskeletal	For both dominant and recessive forms, medical management (eg, with etoricoxib) has been shown to be clinically beneficial related to manifestations affecting multiple organ systems (eg, joint swelling, skin manifestations)	Dermatologic; Gastrointestinal; Musculoskeletal	16283874; 20889364; 22553128; 22331663; 22197487; 28425581; 33852188
Heterozygotes may show mild manifestations

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLCO2A1 gene.

• not provided (9 variants)
• Hypertrophic osteoarthropathy, primary, autosomal recessive, 2 (4 variants)
• Hypertrophic osteoarthropathy, primary, autosomal dominant (2 variants)
• Pachydermoperiostosis syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLCO2A1 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	55	12	68
missense	1	7	78	12	3	101
nonsense	3	2				5
start loss						0
frameshift	5	1				6
inframe indel		1				1
splice donor/acceptor (+/-2bp)	1	2	1			4
splice region		1	4	15	1	21
non coding			3	23	18	44
Total	10	13	83	90	33

Highest pathogenic variant AF is 0.0000197

Variants in SLCO2A1

This is a list of pathogenic ClinVar variants found in the SLCO2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-133934714-C-G			Uncertain significance (Oct 13, 2021)
3-133934722-G-A			Benign (Jan 22, 2024)
3-133934728-C-T			Likely benign (Jul 25, 2023)
3-133934740-G-A			Benign (May 25, 2023)
3-133934746-C-T			Likely benign (Jun 17, 2023)
3-133934772-T-A			Uncertain significance (Aug 17, 2023)
3-133934794-G-C			Likely benign (Jul 18, 2022)
3-133934800-C-T			Likely benign (Sep 10, 2023)
3-133934801-G-A			Uncertain significance (Oct 23, 2022)
3-133934808-A-G			Uncertain significance (Aug 09, 2022)
3-133934818-C-T			Likely benign (Jan 01, 2023)
3-133934832-T-A			Uncertain significance (Jul 05, 2022)
3-133934838-CAGG-C			Likely benign (Apr 13, 2022)
3-133934841-G-A			Likely benign (Nov 05, 2021)
3-133934844-G-A			Likely benign (Oct 17, 2023)
3-133934845-A-C			Likely benign (May 08, 2023)
3-133934941-T-C			Uncertain significance (Jun 10, 2021)
3-133935763-T-A			Likely benign (Dec 29, 2021)
3-133935767-C-T			Likely benign (Aug 23, 2022)
3-133935773-C-T		Hypertrophic osteoarthropathy, primary, autosomal recessive, 2	Pathogenic (Feb 13, 2024)
3-133935776-G-A			Likely benign (Jul 12, 2023)
3-133935780-C-G			Uncertain significance (Nov 01, 2022)
3-133935781-G-A		Hypertrophic osteoarthropathy, primary, autosomal recessive, 2 • Hypertrophic osteoarthropathy, primary, autosomal dominant	Pathogenic/Likely pathogenic (Mar 22, 2022)
3-133935789-T-A			Uncertain significance (Jun 24, 2022)
3-133935790-C-T			Uncertain significance (Nov 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLCO2A1	protein_coding	protein_coding	ENST00000310926	14	119489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.28e-13	0.391	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.518	339	367	0.924	0.0000202	4138
Missense in Polyphen		147	164.69	0.89257		1884
Synonymous	1.08	136	153	0.889	0.00000886	1322
Loss of Function	1.32	24	32.1	0.749	0.00000177	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00132	0.00132
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000984	0.000979
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000984	0.000979
South Asian	0.000166	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May mediate the release of newly synthesized prostaglandins from cells, the transepithelial transport of prostaglandins, and the clearance of prostaglandins from the circulation. Transports PGD2, as well as PGE1, PGE2 and PGF2A.
• Pathway: Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Prostaglandin formation from arachidonate;Transport of organic anions (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.69

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.334
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slco2a1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; renal/urinary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: lipid transport;prostaglandin transport;sodium-independent organic anion transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: lipid transporter activity;prostaglandin transmembrane transporter activity;sodium-independent organic anion transmembrane transporter activity