MFAP2
Basic information
Region (hg38): 1:16974502-16980632
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 MFAP2 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 | 0 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 0 |
Variants in MFAP2
This is a list of pathogenic ClinVar variants found in the MFAP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-16974951-G-C | Likely benign (Nov 01, 2022) | |||
| 1-16975310-A-C | not specified | Uncertain significance (May 11, 2022) | ||
| 1-16975334-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 1-16975337-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
| 1-16975686-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-16976509-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 1-16976710-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 1-16976713-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 1-16976782-C-G | not specified | Uncertain significance (Jan 22, 2024) | ||
| 1-16977114-T-C | not specified | Uncertain significance (May 01, 2024) | ||
| 1-16977172-C-T | not specified | Uncertain significance (Jun 18, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MFAP2 | protein_coding | protein_coding | ENST00000375535 | 8 | 6334 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000427 | 0.632 | 125718 | 0 | 26 | 125744 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 81 | 112 | 0.726 | 0.00000706 | 1186 |
| Missense in Polyphen | 42 | 54.867 | 0.76549 | 580 | ||
| Synonymous | 0.895 | 37 | 44.6 | 0.830 | 0.00000300 | 335 |
| Loss of Function | 0.950 | 10 | 13.8 | 0.724 | 6.78e-7 | 149 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000210 | 0.000210 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000970 | 0.0000967 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the elastin-associated microfibrils.;
- Pathway
- Canonical and Non-canonical Notch signaling;Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation;Notch signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.256
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.905
- hipred
- Y
- hipred_score
- 0.629
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0803
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mfap2
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; skeleton phenotype;
Zebrafish Information Network
- Gene name
- mfap2
- Affected structure
- hyaloid vessel
- Phenotype tag
- abnormal
- Phenotype quality
- hypoplastic
Gene ontology
- Biological process
- extracellular matrix organization;embryonic eye morphogenesis;post-embryonic eye morphogenesis;positive regulation of cold-induced thermogenesis
- Cellular component
- microfibril;extracellular region;collagen-containing extracellular matrix
- Molecular function
- extracellular matrix structural constituent