MFSD3

major facilitator superfamily domain containing 3, the group of Solute carrier family 33

Basic information

Region (hg38): 8:144509070-144511213

Links

ENSG00000167700 ∙ NCBI:113655 ∙ OMIM:620308 ∙ HGNC:25157 ∙ Uniprot:Q96ES6 ∙ 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 MFSD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD3 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			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in MFSD3

This is a list of pathogenic ClinVar variants found in the MFSD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144509364-C-T		not specified	Uncertain significance (Jan 24, 2024)
8-144509403-G-A		not specified	Uncertain significance (Oct 12, 2021)
8-144509448-C-T		not specified	Uncertain significance (Nov 17, 2022)
8-144509451-G-A		not specified	Uncertain significance (Oct 16, 2023)
8-144509467-T-C		not specified	Uncertain significance (May 09, 2022)
8-144509475-G-A		not specified	Likely benign (Feb 15, 2023)
8-144509545-C-T		not specified	Uncertain significance (Oct 05, 2022)
8-144509665-G-A		not specified	Uncertain significance (May 31, 2023)
8-144509734-C-G		not specified	Uncertain significance (Mar 29, 2022)
8-144509737-G-A		not specified	Uncertain significance (Dec 28, 2023)
8-144509770-G-C		not specified	Uncertain significance (Oct 26, 2022)
8-144509818-C-T		not specified	Uncertain significance (Sep 27, 2021)
8-144509829-C-T		not specified	Uncertain significance (Sep 22, 2022)
8-144509832-T-C		not specified	Uncertain significance (Mar 22, 2023)
8-144509872-T-A		not specified	Uncertain significance (Apr 12, 2024)
8-144509880-G-A		not specified	Uncertain significance (Jul 20, 2021)
8-144509928-C-T		not specified	Uncertain significance (Jul 13, 2022)
8-144509947-T-C		not specified	Uncertain significance (Dec 11, 2023)
8-144509959-T-G		not specified	Uncertain significance (Mar 16, 2022)
8-144509977-C-A		not specified	Uncertain significance (Feb 27, 2024)
8-144510419-C-T		not specified	Uncertain significance (Jun 27, 2023)
8-144510422-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-144510447-G-A		not specified	Uncertain significance (Sep 06, 2022)
8-144510450-C-A		not specified	Uncertain significance (Apr 15, 2024)
8-144510629-C-T		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD3	protein_coding	protein_coding	ENST00000301327	5	2140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.86e-12	0.0105	125409	0	80	125489	0.000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.39	264	208	1.27	0.0000102	2451
Missense in Polyphen		115	89.436	1.2858		1179
Synonymous	-3.18	155	112	1.38	0.00000597	1034
Loss of Function	-0.954	15	11.5	1.30	4.93e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000657	0.000643
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.00162	0.00158
Finnish	0.00	0.00
European (Non-Finnish)	0.000255	0.000247
Middle Eastern	0.00162	0.00158
South Asian	0.000285	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.197
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfsd3

Gene ontology

• Biological process: proton transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: solute:proton symporter activity