SLC49A4

protein-coding

solute carrier family 49 member 4, the group of Solute carrier family 49

Gene summary

This gene encodes a membrane-bound protein from the major facilitator superfamily of transporters. Disruption of this gene by translocation has been associated with haplo-insufficiency and renal cell carcinomas. Alternatively spliced transcript variants have been described, but their biological validity has not yet been determined. [provided by RefSeq, Jul 2008]

Previous symbols:

DIRC2

MANE transcript

NM_032839.3

Inheritance

—

ClinVar variants

U:68B:4

Top phenotype

Ovarian cancer

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr3:122,795,069-122,881,139

External References & Databases

Ensembl (ENSG00000138463)

Transcript & Mutation Effects

hg38 • Region Span ~86.1 kb

Loading mutation effect viewer...

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 SLC49A4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

Ovarian cancerTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032839.3. 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			4 clinvar			4
missense			59 clinvar	2 clinvar	2 clinvar	63
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	68	2	2	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032839.3	RefSeq	NP_116228.1	9	MANE Select
ENST00000261038.6	Ensembl	ENSP00000261038.5	9	MANE Select
ENST00000477647.1	Ensembl	ENSP00000418554.1	2	Standard
ENST00000864462.1	Ensembl	ENSP00000534521.1	10	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261038
Coding exons: 9
Length: 86345
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125748
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	188	247	0.763	0.0000124	3026
Missense (PolyPhen)		34	51.167	0.66449		654
Synonymous	0.453	92	97.7	0.942	0.00000526	1034
Loss of Function	1.01	16	21.0	0.761	0.00000103	251

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0.00010	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Electrogenic metabolite transporter. {ECO:0000269|PubMed:21692750}.;
Disease: DISEASE: Note=A chromosomal aberration involving DIRC2 has been found in a family with renal carcinoma. Translocation t(2;3)(q35;q21) (PubMed:11912179). {ECO:0000269|PubMed:11912179}.;

Recessive Scores

pRec: 0.0829

Intolerance Scores

RVIS EVS: -0.29
RVIS percentile EVS: 32.94

Essentials

Essential (gene trap): N