MFSD12

major facilitator superfamily domain containing 12

Basic information

Region (hg38): 19:3538261-3574290

Previous symbols: [ "C19orf28" ]

Links

ENSG00000161091 ∙ NCBI:126321 ∙ OMIM:617745 ∙ HGNC:28299 ∙ Uniprot:Q6NUT3 ∙ 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 MFSD12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFSD12 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	2	3
missense				2		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	0	3	4

Variants in MFSD12

This is a list of pathogenic ClinVar variants found in the MFSD12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3543246-T-C		not specified	Uncertain significance (Sep 16, 2021)
19-3543291-C-T		not specified	Uncertain significance (Nov 09, 2021)
19-3543317-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-3543329-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-3543382-C-G			Likely benign (Mar 01, 2023)
19-3543480-G-GC		not specified	Benign (Mar 29, 2016)
19-3543646-G-C			Likely benign (Apr 01, 2022)
19-3543669-G-T		not specified	Uncertain significance (Jul 21, 2021)
19-3543910-C-T		not specified	Uncertain significance (Aug 09, 2021)
19-3543934-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-3543934-G-C		not specified	Uncertain significance (Dec 19, 2023)
19-3543982-C-T			Benign (Sep 01, 2023)
19-3544006-G-A		not specified	Uncertain significance (Nov 09, 2021)
19-3544876-G-A			Benign (Feb 26, 2018)
19-3545024-C-T		MFSD12 POLYMORPHISM	Benign (Jan 10, 2019)
19-3546187-G-A			Benign (Mar 19, 2019)
19-3546266-C-T			Likely benign (Apr 01, 2023)
19-3546337-G-A			Likely benign (Apr 01, 2022)
19-3546342-G-A			Benign (Nov 01, 2019)
19-3551127-C-T			Likely benign (Oct 01, 2023)
19-3573344-C-T		not specified	Uncertain significance (Jan 16, 2025)
19-3573708-G-A		not specified	Uncertain significance (Jul 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFSD12	protein_coding	protein_coding	ENST00000398558	10	36030

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.73e-18	0.00379	124628	0	218	124846	0.000873

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.74	459	321	1.43	0.0000197	3348
Missense in Polyphen		151	105.14	1.4362		1143
Synonymous	-3.91	214	153	1.40	0.0000106	1155
Loss of Function	-0.115	26	25.4	1.02	0.00000133	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000758	0.000755
Ashkenazi Jewish	0.00832	0.00827
East Asian	0.000113	0.000111
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000800	0.000777
Middle Eastern	0.000113	0.000111
South Asian	0.000558	0.000556
Other	0.000673	0.000659

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.98

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.219
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfsd12
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; pigmentation phenotype

Zebrafish Information Network

• Gene name: mfsd12a
• Affected structure: xanthophore
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: carbohydrate transport;transmembrane transport;organic substance transport
• Cellular component: lysosomal membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: transporter activity;symporter activity