SLC49A3

solute carrier family 49 member 3, the group of Solute carrier family 49

Basic information

Region (hg38): 4:681828-689271

Previous symbols: [ "MFSD7" ]

Links

ENSG00000169026 ∙ NCBI:84179 ∙ ∙ HGNC:26177 ∙ Uniprot:Q6UXD7 ∙ 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 SLC49A3 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC49A3 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	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	17	1	0

Variants in SLC49A3

This is a list of pathogenic ClinVar variants found in the SLC49A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-681929-G-A		not specified	Uncertain significance (May 17, 2023)
4-681929-G-C		not specified	Uncertain significance (Sep 14, 2023)
4-681930-C-T		not specified	Uncertain significance (Mar 07, 2024)
4-681951-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-682004-G-C		not specified	Uncertain significance (Oct 04, 2022)
4-682061-G-A		not specified	Uncertain significance (Sep 27, 2022)
4-682080-C-G		not specified	Uncertain significance (Nov 18, 2022)
4-682082-T-G		not specified	Uncertain significance (Jun 22, 2021)
4-682088-C-T		not specified	Uncertain significance (Dec 17, 2021)
4-682116-G-A		not specified	Uncertain significance (Dec 16, 2022)
4-682181-G-T		not specified	Uncertain significance (Apr 26, 2023)
4-682187-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-682247-C-T		not specified	Uncertain significance (Dec 13, 2022)
4-682272-G-A		not specified	Likely benign (Oct 10, 2023)
4-682301-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-682356-C-T		not specified	Uncertain significance (Aug 10, 2021)
4-682828-G-A		not specified	Uncertain significance (Sep 17, 2021)
4-682883-C-T		not specified	Uncertain significance (Jul 19, 2022)
4-683232-T-C		not specified	Likely benign (Nov 29, 2023)
4-683238-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-683270-G-A		not specified	Uncertain significance (Apr 25, 2023)
4-683313-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-683321-G-A		not specified	Uncertain significance (Mar 01, 2023)
4-683352-C-T		not specified	Uncertain significance (May 31, 2023)
4-683649-C-G		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC49A3	protein_coding	protein_coding	ENST00000322224	10	7613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.10e-18	0.000647	125568	1	133	125702	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.762	345	307	1.12	0.0000186	3470
Missense in Polyphen		76	67.389	1.1278		753
Synonymous	-1.59	171	147	1.17	0.0000101	1249
Loss of Function	-1.01	24	19.2	1.25	9.84e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000713	0.000694
Ashkenazi Jewish	0.00	0.00
East Asian	0.000549	0.000544
Finnish	0.0000962	0.0000924
European (Non-Finnish)	0.000400	0.000361
Middle Eastern	0.000549	0.000544
South Asian	0.00211	0.00203
Other	0.000510	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.0467
• hipred: N
• hipred_score: 0.170
• ghis: 0.492

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mfsd7a

Gene ontology

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