GeneBe

MFAP1

microfibril associated protein 1, the group of Spliceosomal B complex

Basic information

Region (hg38): 15:43804492-43824690

Links

ENSG00000140259 ∙ NCBI:4236 ∙ OMIM:600215 ∙ HGNC:7032 ∙ Uniprot:P55081 ∙ 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 MFAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFAP1 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
4
clinvar
 4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 4 0 0

Variants in MFAP1

This is a list of pathogenic ClinVar variants found in the MFAP1 region.

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

Position Type Phenotype Significance ClinVar
15-43805107-C-T not specified Uncertain significance (Oct 12, 2021)2206073
15-43805396-T-C not specified Uncertain significance (Sep 16, 2021)2250187
15-43809835-C-T not specified Uncertain significance (Apr 27, 2024)3294491
15-43813077-T-C not specified Uncertain significance (Apr 22, 2024)3294492
15-43814629-C-G not specified Uncertain significance (Sep 14, 2022)2311984
15-43817248-T-G not specified Uncertain significance (Dec 30, 2023)3125644

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MFAP1protein_codingprotein_codingENST00000267812 920311
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.7960.204125737091257460.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.741412670.5280.00001652904
Missense in Polyphen2065.7120.30436726
Synonymous-1.109683.21.150.00000404784
Loss of Function4.22631.60.1900.00000231310

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005790.0000579
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00009270.0000924
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome. {ECO:0000269|PubMed:28781166}.;
Pathway
Canonical and Non-canonical Notch signaling;Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation (Consensus)

Recessive Scores

pRec
0.117

Intolerance Scores

loftool
0.114
rvis_EVS
0.1
rvis_percentile_EVS
61.49

Haploinsufficiency Scores

pHI
0.136
hipred
Y
hipred_score
0.746
ghis
0.576

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.947

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mfap1b
Phenotype

Gene ontology

Biological process
mRNA splicing, via spliceosome
Cellular component
microfibril;extracellular region;nucleus;U2-type precatalytic spliceosome
Molecular function
RNA binding;protein binding