MFSD13A

major facilitator superfamily domain containing 13A

Basic information

Region (hg38): 10:102461395-102477045

Previous symbols: [ "C10orf77", "TMEM180" ]

Links

ENSG00000138111 ∙ NCBI:79847 ∙ OMIM:620255 ∙ HGNC:26196 ∙ Uniprot:Q14CX5 ∙ 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 MFSD13A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD13A 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				1		1
missense			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	2	0

Variants in MFSD13A

This is a list of pathogenic ClinVar variants found in the MFSD13A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-102471284-A-T		not specified	Uncertain significance (Oct 29, 2021)
10-102471332-G-A		not specified	Likely benign (Jul 06, 2021)
10-102473825-C-T			Likely benign (Dec 01, 2022)
10-102473849-G-C		not specified	Uncertain significance (Jul 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD13A	protein_coding	protein_coding	ENST00000238936	8	15654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0495	0.950	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.400	296	316	0.937	0.0000202	3302
Missense in Polyphen		110	119.34	0.92174		1331
Synonymous	-0.211	150	147	1.02	0.00000932	1147
Loss of Function	2.92	6	20.1	0.298	9.50e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -1.38
• rvis_percentile_EVS: 4.39

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.294
• ghis: 0.579

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mfsd13a

Gene ontology

• Cellular component: integral component of membrane