MDFI
Basic information
Region (hg38): 6:41636882-41654244
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 19 | 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:
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:
- 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