SLC22A25

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

Basic information

Region (hg38): 11:63158437-63243599

Links

ENSG00000196600 ∙ NCBI:387601 ∙ OMIM:610792 ∙ HGNC:32935 ∙ Uniprot:Q6T423 ∙ 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 SLC22A25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A25 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				4		4
missense			31	7		38
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region				1		1
non coding						0
Total	0	0	31	12	1

Variants in SLC22A25

This is a list of pathogenic ClinVar variants found in the SLC22A25 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63163840-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-63163897-A-G		not specified	Likely benign (Sep 17, 2021)
11-63163903-G-C		not specified	Uncertain significance (Nov 23, 2024)
11-63163912-C-G		not specified	Uncertain significance (Jan 20, 2023)
11-63163939-A-G		not specified	Uncertain significance (Sep 13, 2023)
11-63163951-A-G		not specified	Uncertain significance (Mar 23, 2023)
11-63163966-T-C		not specified	Uncertain significance (Jan 26, 2023)
11-63163999-C-T		not specified	Uncertain significance (Aug 10, 2021)
11-63164000-T-C		not specified	Uncertain significance (Apr 04, 2024)
11-63164029-C-T		not specified	Uncertain significance (Mar 11, 2024)
11-63164032-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-63164045-A-G		not specified	Uncertain significance (Apr 22, 2022)
11-63164069-T-G		SLC22A25-related disorder	Likely benign (Jun 13, 2019)
11-63164533-T-C		not specified	Likely benign (Jul 14, 2023)
11-63166073-C-T		not specified	Uncertain significance (Dec 05, 2022)
11-63166098-G-T		not specified	Uncertain significance (Oct 05, 2021)
11-63166102-C-A		not specified	Uncertain significance (Aug 04, 2022)
11-63166103-T-G		not specified	Uncertain significance (Aug 04, 2022)
11-63166148-C-G		not specified	Uncertain significance (Nov 15, 2024)
11-63166193-A-G		not specified	Uncertain significance (Jun 10, 2022)
11-63166217-A-G		not specified	Uncertain significance (Aug 22, 2023)
11-63166236-A-C		not specified	Uncertain significance (Apr 25, 2022)
11-63180679-A-G		not specified	Uncertain significance (Jul 09, 2021)
11-63180699-G-A		not specified	Uncertain significance (Sep 12, 2024)
11-63180747-A-G		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A25	protein_coding	protein_coding	ENST00000306494	9	65877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-16	0.00292	120825	363	4555	125743	0.0198

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.44	372	302	1.23	0.0000151	3577
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.258	0.217
Ashkenazi Jewish	0.0124	0.00917
East Asian	0.00122	0.00120
Finnish	0.00602	0.00602
European (Non-Finnish)	0.0100	0.00957
Middle Eastern	0.00122	0.00120
South Asian	0.00397	0.00370
Other	0.0190	0.0149

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.26

Haploinsufficiency Scores

• pHI: 0.0640
• hipred: N
• hipred_score: 0.112
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0472

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc22a30

Gene ontology

• Biological process: transmembrane transport
• Cellular component: integral component of membrane