MFSD6

major facilitator superfamily domain containing 6

Basic information

Region (hg38): 2:190408354-190509205

Links

ENSG00000151690 ∙ NCBI:54842 ∙ OMIM:613476 ∙ HGNC:24711 ∙ Uniprot:Q6ZSS7 ∙ 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 MFSD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD6 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					3	3
missense			37	1	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	4

Variants in MFSD6

This is a list of pathogenic ClinVar variants found in the MFSD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-190436114-A-G		not specified	Uncertain significance (May 31, 2023)
2-190436190-T-C			Benign (Feb 09, 2018)
2-190436227-C-T			Benign (Dec 19, 2017)
2-190436282-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-190436304-A-G		not specified	Uncertain significance (Feb 15, 2023)
2-190436358-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-190436516-A-G		not specified	Uncertain significance (Feb 23, 2023)
2-190436615-C-T		not specified	Uncertain significance (Dec 06, 2021)
2-190436762-A-T		not specified	Uncertain significance (Jul 09, 2021)
2-190436796-C-T		not specified	Uncertain significance (Jun 30, 2022)
2-190436823-C-T		not specified	Uncertain significance (Nov 01, 2022)
2-190436846-G-T		not specified	Uncertain significance (Mar 29, 2022)
2-190436851-A-C		not specified	Uncertain significance (May 11, 2022)
2-190436914-C-T			Benign (Mar 29, 2018)
2-190436933-A-T		not specified	Uncertain significance (Aug 09, 2021)
2-190436951-A-G		not specified	Uncertain significance (Dec 06, 2022)
2-190436974-G-A			Benign (Dec 19, 2017)
2-190437062-G-A		not specified	Uncertain significance (Oct 22, 2021)
2-190437063-G-C		not specified	Uncertain significance (Apr 06, 2024)
2-190437135-A-G		not specified	Uncertain significance (May 30, 2023)
2-190437158-G-A		not specified	Uncertain significance (Jul 09, 2021)
2-190437203-C-T		not specified	Uncertain significance (Jun 07, 2024)
2-190437204-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-190437237-G-C		not specified	Uncertain significance (Nov 17, 2023)
2-190437245-G-T		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD6	protein_coding	protein_coding	ENST00000392328	6	100851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000329	0.987	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	335	440	0.762	0.0000247	5170
Missense in Polyphen		57	121.41	0.46946		1485
Synonymous	-0.461	176	168	1.05	0.0000103	1612
Loss of Function	2.24	13	25.1	0.517	0.00000117	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000152
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.0000545	0.0000544
South Asian	0.000229	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.500
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.543
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0229

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfsd6

Gene ontology

• Cellular component: membrane;integral component of membrane