SLC22A23

protein-coding

solute carrier family 22 member 23, the group of Solute carrier family 22

Gene summary

SLC22A23 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 2008]

Previous symbols:

C6orf85

MANE transcript

NM_015482.2

Inheritance

—

ClinVar variants

U:101B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr6:3,268,962-3,457,050

External References & Databases

Ensembl (ENSG00000137266)

Transcript & Mutation Effects

hg38 • Region Span ~188.1 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 SLC22A23 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 97

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015482.2. 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	2 clinvar	7
missense			97 clinvar	2 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	101	5	2	108

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015482.2	RefSeq	NP_056297.1	10	MANE Select
ENST00000406686.8	Ensembl	ENSP00000385028.3	10	MANE Select
NM_001286455.1	RefSeq	NP_001273384.1	8	Standard
NM_001286456.2	RefSeq	NP_001273385.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ion transport
transmembrane transport

Molecular Function

protein binding
transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000406686
Coding exons: 10
Length: 188061
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125739
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.87	292	397	0.735	0.0000231	4409
Missense (PolyPhen)		87	156.67	0.55531		1687
Synonymous	-0.613	194	183	1.06	0.0000119	1469
Loss of Function	4.01	5	27.8	0.180	0.00000174	277

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000084	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000058	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.429
RVIS EVS: -0.87
RVIS percentile EVS: 10.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.375

Gene Damage Prediction

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