MFAP1
protein-codingmicrofibril associated protein 1, the group of Spliceosomal B complex
Gene summary
Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in microfibril and nucleoplasm. Part of U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MFAP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005926.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 26 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 28 | 1 | 0 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005917.2 | 9 | MANE Select | |
| Ensembl | ENSP00000267812.3 | 9 | MANE Select | |
| Ensembl | ENSP00000610108.1 | 9 | Standard | |
| Ensembl | ENSP00000610108.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Canonical and Non-canonical Notch signaling
- Extracellular matrix organization
- Molecules associated with elastic fibres
- Elastic fibre formation
Biological Process
- mRNA splicing, via spliceosome
Molecular Function
- RNA binding
- protein binding
Cellular Component
- microfibril
- extracellular region
- nucleus
- U2-type precatalytic spliceosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000267812
- Coding exons
- 9
- Length
- 20311
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125746
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.74 | 141 | 267 | 0.528 | 0.0000165 | 2904 |
| Missense (PolyPhen) | 20 | 65.712 | 0.30436 | 726 | ||
| Synonymous | -1.10 | 96 | 83.2 | 1.15 | 0.00000404 | 784 |
| Loss of Function | 4.22 | 6 | 31.6 | 0.190 | 0.00000231 | 310 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome. {ECO:0000269|PubMed:28781166}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.114
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 61.49
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.947
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |