MFSD1

major facilitator superfamily domain containing 1

Basic information

Region (hg38): 3:158732197-158829719

Links

ENSG00000118855 ∙ NCBI:64747 ∙ OMIM:619976 ∙ HGNC:25874 ∙ Uniprot:Q9H3U5 ∙ 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 MFSD1 gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD1 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	15	1	0

Variants in MFSD1

This is a list of pathogenic ClinVar variants found in the MFSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-158732207-A-T		not specified	Uncertain significance (May 05, 2023)
3-158732270-G-A		not specified	Uncertain significance (Dec 19, 2023)
3-158732279-G-C		not specified	Uncertain significance (Jan 26, 2022)
3-158732291-T-G		not specified	Uncertain significance (Jun 11, 2021)
3-158732292-C-G		not specified	Uncertain significance (Sep 16, 2021)
3-158732298-A-C		not specified	Uncertain significance (Jul 09, 2021)
3-158732382-A-G		not specified	Likely benign (Jan 17, 2023)
3-158732382-A-T		not specified	Likely benign (Sep 01, 2021)
3-158802043-T-C		not specified	Uncertain significance (Dec 27, 2023)
3-158802043-T-G		not specified	Uncertain significance (Jan 26, 2023)
3-158802076-C-T		not specified	Uncertain significance (Jan 06, 2023)
3-158802110-T-G		not specified	Likely benign (Aug 10, 2021)
3-158802232-C-G		not specified	Uncertain significance (Jan 22, 2024)
3-158804370-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-158805458-C-G		not specified	Uncertain significance (Dec 27, 2023)
3-158805462-T-C		not specified	Uncertain significance (Dec 11, 2023)
3-158807396-G-A		not specified	Uncertain significance (Sep 18, 2023)
3-158807406-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-158809219-G-A		not specified	Uncertain significance (Mar 01, 2024)
3-158809220-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-158814005-C-G		not specified	Uncertain significance (Nov 10, 2022)
3-158814035-G-T		not specified	Uncertain significance (Oct 03, 2023)
3-158814046-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-158814062-T-C		not specified	Uncertain significance (Jan 03, 2024)
3-158819658-C-T		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD1	protein_coding	protein_coding	ENST00000415822	16	97522

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.33e-17	0.0187	125595	0	153	125748	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0244	280	279	1.00	0.0000132	3315
Missense in Polyphen		49	50.256	0.97501		582
Synonymous	-0.923	117	105	1.11	0.00000514	1021
Loss of Function	0.476	27	29.8	0.906	0.00000154	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.00111	0.00109
East Asian	0.000436	0.000435
Finnish	0.000371	0.000370
European (Non-Finnish)	0.000743	0.000739
Middle Eastern	0.000436	0.000435
South Asian	0.000297	0.000294
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.804
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.251
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.574

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfsd1

Gene ontology

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