MDFI

MyoD family inhibitor

Basic information

Region (hg38): 6:41636882-41654244

Links

ENSG00000112559 ∙ NCBI:4188 ∙ OMIM:604971 ∙ HGNC:6967 ∙ Uniprot:Q99750 ∙ 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 MDFI gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDFI 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			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	1

Variants in MDFI

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

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

Position	Type	Phenotype	Significance	ClinVar
6-41638822-C-T		not specified	Uncertain significance (Dec 06, 2024)
6-41646158-G-A		not specified	Uncertain significance (Oct 10, 2023)
6-41646178-C-A		not specified	Uncertain significance (Jun 18, 2021)
6-41646219-C-T		not specified	Uncertain significance (Apr 11, 2023)
6-41646256-C-T			Likely benign (Jun 08, 2018)
6-41646285-A-G		not specified	Uncertain significance (Nov 28, 2023)
6-41649637-C-G		not specified	Uncertain significance (Nov 15, 2021)
6-41649706-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-41649724-G-A		not specified	Uncertain significance (May 18, 2023)
6-41649742-G-A			Benign (Jun 08, 2018)
6-41649750-C-A		not specified	Uncertain significance (Jul 14, 2021)
6-41649788-G-C		not specified	Uncertain significance (Mar 22, 2023)
6-41649790-G-C		not specified	Uncertain significance (Aug 07, 2024)
6-41653320-C-G		not specified	Uncertain significance (Aug 20, 2024)
6-41653346-G-A		not specified	Uncertain significance (Feb 26, 2024)
6-41653367-C-A		not specified	Uncertain significance (Feb 12, 2024)
6-41653375-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-41653413-C-G		not specified	Uncertain significance (Apr 20, 2024)
6-41653456-G-C		not specified	Uncertain significance (Jun 17, 2024)
6-41653489-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-41653537-A-G		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDFI	protein_coding	protein_coding	ENST00000230321	4	17365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.334	0.653	125701	0	15	125716	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.124	134	138	0.970	0.00000794	1570
Missense in Polyphen		42	53.174	0.78987		660
Synonymous	-1.02	74	63.7	1.16	0.00000457	500
Loss of Function	2.08	2	8.58	0.233	3.70e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000443	0.000416
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the transactivation activity of the Myod family of myogenic factors and represses myogenesis. Acts by associating with Myod family members and retaining them in the cytoplasm by masking their nuclear localization signals. Can also interfere with the DNA-binding activity of Myod family members. Plays an important role in trophoblast and chondrogenic differentiation. Regulates the transcriptional activity of TCF7L1/TCF3 by interacting directly with TCF7L1/TCF3 and preventing it from binding DNA. Binds to the axin complex, resulting in an increase in the level of free beta-catenin. Affects axin regulation of the WNT and JNK signaling pathways (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.185

Intolerance Scores

• loftool: 0.275
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.476
• hipred: N
• hipred_score: 0.490
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdfi
• 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); skeleton phenotype; embryo phenotype; respiratory system phenotype; 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); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;dorsal/ventral axis specification;negative regulation of Wnt signaling pathway;cytoplasmic sequestering of transcription factor;negative regulation of DNA binding;embryonic skeletal system morphogenesis;trophoblast giant cell differentiation
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding;transcription factor binding;identical protein binding