SLC22A9

solute carrier family 22 member 9, the group of Solute carrier family 22

Basic information

Region (hg38): 11:63369784-63410294

Links

ENSG00000149742 ∙ NCBI:114571 ∙ OMIM:607579 ∙ HGNC:16261 ∙ Uniprot:Q8IVM8 ∙ 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 SLC22A9 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A9 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in SLC22A9

This is a list of pathogenic ClinVar variants found in the SLC22A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63370070-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-63370139-C-T		not specified	Uncertain significance (Dec 08, 2023)
11-63370187-T-C		not specified	Uncertain significance (Jul 09, 2021)
11-63370241-A-G		not specified	Uncertain significance (Jan 20, 2023)
11-63370393-A-C		not specified	Uncertain significance (Sep 13, 2023)
11-63370394-T-C		not specified	Likely benign (Mar 12, 2024)
11-63370408-G-C		not specified	Uncertain significance (Nov 17, 2022)
11-63370412-G-T		not specified	Uncertain significance (Jan 26, 2022)
11-63370459-G-A			Uncertain significance (Sep 03, 2021)
11-63373735-T-A		not specified	Uncertain significance (Dec 13, 2023)
11-63373744-C-T		not specified	Uncertain significance (Nov 15, 2021)
11-63374019-C-G		not specified	Uncertain significance (Nov 14, 2023)
11-63375673-A-G		not specified	Uncertain significance (Aug 14, 2023)
11-63375732-T-A		not specified	Uncertain significance (May 31, 2023)
11-63406597-C-G		not specified	Uncertain significance (Nov 09, 2021)
11-63406643-G-T		not specified	Uncertain significance (Dec 22, 2023)
11-63406646-C-G		not specified	Uncertain significance (May 16, 2023)
11-63406655-T-C		not specified	Uncertain significance (Jun 26, 2023)
11-63406657-C-T		not specified	Uncertain significance (Nov 13, 2023)
11-63408156-G-A		not specified	Uncertain significance (Apr 26, 2023)
11-63408175-C-A		not specified	Uncertain significance (Oct 25, 2023)
11-63409809-G-A		not specified	Uncertain significance (Sep 23, 2023)
11-63409858-T-G		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A9	protein_coding	protein_coding	ENST00000279178	10	40506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-19	0.000748	125608	1	133	125742	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	364	303	1.20	0.0000149	3632
Missense in Polyphen		78	74.701	1.0442		912
Synonymous	0.427	105	111	0.948	0.00000551	1113
Loss of Function	-0.716	26	22.3	1.16	0.00000108	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000908	0.000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00230	0.00218
Finnish	0.000325	0.000323
European (Non-Finnish)	0.000443	0.000440
Middle Eastern	0.00230	0.00218
South Asian	0.000611	0.000588
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-independent organic anion transporter which exhibits high specificity for sulfated conjugates of xenobiotics and steroid hormones. It is also specifically activated by 3 to 5 carbons-containing short-chain fatty acids/SCFAs, including propionate, butyrate and valerate. May operate the exchange of sulfated organic components against short-chain fatty acids/SCFAs at the sinusoidal membrane of hepatocytes. {ECO:0000269|PubMed:17393504}.

Intolerance Scores

• loftool: 0.955
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.17

Haploinsufficiency Scores

• pHI: 0.0344
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.353

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a30

Gene ontology

• Biological process: hormone transport;short-chain fatty acid import;sodium-independent organic anion transport;anion transmembrane transport
• Cellular component: integral component of membrane;basolateral plasma membrane
• Molecular function: anion:anion antiporter activity;sodium-independent organic anion transmembrane transporter activity;short-chain fatty acid transmembrane transporter activity