MFSD9

major facilitator superfamily domain containing 9

Basic information

Region (hg38): 2:102714629-102736888

Links

ENSG00000135953 ∙ NCBI:84804 ∙ OMIM:620301 ∙ HGNC:28158 ∙ Uniprot:Q8NBP5 ∙ 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 MFSD9 gene.

• Inborn genetic diseases (32 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD9 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	1	3	35
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	1	3

Variants in MFSD9

This is a list of pathogenic ClinVar variants found in the MFSD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-102718461-G-T		not specified	Uncertain significance (Dec 20, 2023)
2-102718521-G-C		not specified	Uncertain significance (Nov 13, 2023)
2-102718524-G-C			Benign (Jun 11, 2018)
2-102718527-C-T		not specified	Uncertain significance (Jan 27, 2022)
2-102718535-C-G		not specified	Uncertain significance (Mar 16, 2022)
2-102718551-C-T		not specified	Uncertain significance (Oct 05, 2021)
2-102718556-G-C		not specified	Uncertain significance (Jan 23, 2023)
2-102718578-G-A		not specified	Uncertain significance (Aug 28, 2023)
2-102718658-G-A		not specified	Uncertain significance (Apr 18, 2023)
2-102718667-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-102718691-G-T		not specified	Uncertain significance (Jan 08, 2024)
2-102718719-C-T			Benign (Jun 11, 2018)
2-102718764-T-A		not specified	Uncertain significance (Jul 19, 2022)
2-102718794-G-T		not specified	Uncertain significance (Jul 11, 2023)
2-102718833-C-T		not specified	Uncertain significance (Mar 28, 2023)
2-102718857-T-C		not specified	Uncertain significance (Sep 12, 2023)
2-102718872-T-G		not specified	Uncertain significance (Dec 11, 2023)
2-102718904-A-G		not specified	Uncertain significance (May 17, 2023)
2-102718907-C-T		not specified	Uncertain significance (Jul 13, 2021)
2-102718908-G-A		not specified	Uncertain significance (Oct 29, 2021)
2-102718956-T-C		not specified	Likely benign (Sep 27, 2021)
2-102718983-T-C		not specified	Uncertain significance (Dec 20, 2023)
2-102719003-A-G		not specified	Uncertain significance (Apr 19, 2023)
2-102719021-C-T		not specified	Likely benign (Oct 17, 2023)
2-102719071-C-A		not specified	Uncertain significance (Apr 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD9	protein_coding	protein_coding	ENST00000258436	6	21049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.35e-10	0.0880	125342	4	402	125748	0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.800	318	280	1.13	0.0000159	3014
Missense in Polyphen		86	81.713	1.0525		921
Synonymous	-2.13	151	121	1.25	0.00000710	1056
Loss of Function	0.0463	14	14.2	0.987	6.87e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00134
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00147	0.00146
Middle Eastern	0.000217	0.000217
South Asian	0.00626	0.00619
Other	0.00180	0.00179

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.461
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.63

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.219
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0196

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfsd9

Gene ontology

• Biological process: transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: transporter activity