SLC49A4

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

Basic information

Region (hg38): 3:122795068-122881139

Previous symbols: [ "DIRC2" ]

Links

ENSG00000138463 ∙ NCBI:84925 ∙ OMIM:602773 ∙ HGNC:16628 ∙ Uniprot:Q96SL1 ∙ 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 SLC49A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC49A4 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			22		2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	2

Variants in SLC49A4

This is a list of pathogenic ClinVar variants found in the SLC49A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-122795250-G-C		not specified	Uncertain significance (Aug 22, 2023)
3-122795254-C-G		not specified	Uncertain significance (Dec 14, 2022)
3-122795268-T-A		not specified	Uncertain significance (Nov 09, 2021)
3-122795286-G-A		not specified	Uncertain significance (Apr 13, 2023)
3-122795299-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-122795304-C-T		Ovarian cancer	Benign (Jan 01, 2022)
3-122795325-G-T		not specified	Uncertain significance (Feb 17, 2024)
3-122795449-C-T		not specified	Uncertain significance (Jun 03, 2024)
3-122795499-C-T		not specified	Uncertain significance (May 31, 2023)
3-122806910-C-G		not specified	Uncertain significance (May 09, 2023)
3-122806919-A-G		not specified	Uncertain significance (Jan 10, 2023)
3-122806925-A-G		not specified	Likely benign (Apr 09, 2024)
3-122826927-C-T		not specified	Uncertain significance (Aug 14, 2023)
3-122827042-G-A		not specified	Uncertain significance (Dec 15, 2021)
3-122833392-T-C		not specified	Uncertain significance (May 05, 2023)
3-122833422-G-A		not specified	Uncertain significance (Feb 22, 2023)
3-122860128-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-122860149-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-122860191-C-T		not specified	Uncertain significance (Aug 13, 2021)
3-122860196-A-T		not specified	Uncertain significance (May 10, 2024)
3-122860197-C-A		Ovarian cancer	Benign (Jan 01, 2022)
3-122872465-G-A		Ovarian cancer • not specified	Conflicting classifications of pathogenicity (Feb 10, 2022)
3-122872468-C-T		not specified	Uncertain significance (Jan 31, 2023)
3-122872472-T-C		not specified	Uncertain significance (May 11, 2022)
3-122879290-C-T		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC49A4	protein_coding	protein_coding	ENST00000261038	9	86345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-9	0.447	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	188	247	0.763	0.0000124	3026
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000427	0.000426
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000900	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000102	0.0000980
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.502
• ghis: 0.426

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Dirc2