MDFIC

MyoD family inhibitor domain containing

Basic information

Region (hg38): 7:114922094-115019917

Links

ENSG00000135272 ∙ NCBI:29969 ∙ OMIM:614511 ∙ HGNC:28870 ∙ Uniprot:Q9P1T7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lymphatic malformation 12 (Moderate), mode of inheritance: AR
• lymphatic malformation 12 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lymphatic malformation 12	AR	Cardiovascular	Individuals have been described as having lymphatic and other cardiovascular anomalies, and awareness may enable early diagnosis and medical and/or surgical management related to the malformations	Cardiovascular	35235341

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MDFIC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDFIC 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				2		2
missense			17	3		20
nonsense						0
start loss			2			2
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9			9
Total	0	2	28	5	0

Variants in MDFIC

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

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

Position	Type	Phenotype	Significance	ClinVar
7-114922427-T-A		Inborn genetic diseases	Uncertain significance (Oct 22, 2021)
7-114922435-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2023)
7-114922436-C-A		Inborn genetic diseases	Uncertain significance (May 24, 2023)
7-114922441-G-A		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
7-114922475-T-A		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
7-114922505-G-A		Inborn genetic diseases	Uncertain significance (Nov 10, 2024)
7-114922519-G-A		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
7-114922520-T-A		Inborn genetic diseases	Uncertain significance (May 23, 2023)
7-114922546-G-T		Inborn genetic diseases	Uncertain significance (Apr 09, 2024)
7-114922556-G-C		Inborn genetic diseases	Uncertain significance (Oct 09, 2024)
7-114922570-T-C		Inborn genetic diseases	Uncertain significance (Aug 29, 2023)
7-114922583-AGAG-A		MDFIC-related disorder	Likely benign (Jun 13, 2024)
7-114922594-A-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2024)
7-114922628-G-T		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
7-114922936-G-T		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
7-114922989-C-G		Inborn genetic diseases	Uncertain significance (Nov 21, 2024)
7-114923034-A-C		Inborn genetic diseases	Uncertain significance (Mar 11, 2022)
7-114923035-T-A		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)
7-114923070-G-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
7-114923125-A-G		Inborn genetic diseases	Uncertain significance (Aug 12, 2024)
7-114942305-A-C		Inborn genetic diseases	Uncertain significance (May 29, 2024)
7-114942305-A-G		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
7-114942309-A-G		Inborn genetic diseases	Uncertain significance (Dec 27, 2022)
7-114942347-T-A		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
7-114942359-C-T			Likely benign (Dec 19, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDFIC	protein_coding	protein_coding	ENST00000257724	5	97048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0376	0.932	125645	0	57	125702	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.289	167	157	1.06	0.00000756	2254
Missense in Polyphen		76	68.634	1.1073		890
Synonymous	-0.102	60	59.0	1.02	0.00000313	721
Loss of Function	1.88	4	10.6	0.377	4.46e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000163	0.000163
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000283	0.000282
Middle Eastern	0.000163	0.000163
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional activator or repressor. Inhibits the transcriptional activation of Zic family proteins ZIC1, ZIC2 and ZIC3. Retains nuclear Zic proteins ZIC1, ZIC2 and ZIC3 in the cytoplasm. Modulates the expression from both cellular and viral promoters. Down-regulates Tat-dependent transcription of the human immunodeficiency virus type 1 (HIV-1) LTR by interacting with HIV-1 Tat and Rev and impairing their nuclear import, probably by rendering the NLS domains inaccessible to importin- beta. Also stimulates activation of human T-cell leukemia virus type I (HTLV-I) LTR. 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. {ECO:0000269|PubMed:10671520, ECO:0000269|PubMed:12192039, ECO:0000269|PubMed:12944466, ECO:0000269|PubMed:16260749, ECO:0000269|Ref.6}.
• Pathway: Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.185

Haploinsufficiency Scores

• pHI: 0.102
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdfic

Gene ontology

• Biological process: activation of JUN kinase activity;viral process;regulation of Wnt signaling pathway;negative regulation of protein import into nucleus;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of viral transcription
• Cellular component: nucleus;nucleolus;cytoplasm
• Molecular function: protein binding;transcription factor binding;cyclin binding;Tat protein binding