MFAP4

microfibril associated protein 4, the group of Fibrinogen C domain containing

Basic information

Region (hg38): 17:19383442-19387190

Links

ENSG00000166482 ∙ NCBI:4239 ∙ OMIM:600596 ∙ HGNC:7035 ∙ Uniprot:P55083 ∙ 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 MFAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFAP4 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in MFAP4

This is a list of pathogenic ClinVar variants found in the MFAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-19384469-C-T		not specified	Uncertain significance (Nov 17, 2023)
17-19384661-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-19384665-C-T		not specified	Uncertain significance (Nov 03, 2022)
17-19385153-C-T		not specified	Uncertain significance (Jun 21, 2023)
17-19385207-T-A		not specified	Uncertain significance (Jan 26, 2022)
17-19385215-A-G		not specified	Uncertain significance (Jun 22, 2023)
17-19386321-C-T		not specified	Uncertain significance (Oct 06, 2021)
17-19386333-T-G		not specified	Uncertain significance (Jun 28, 2023)
17-19386347-A-G		not specified	Uncertain significance (Jun 07, 2024)
17-19386384-G-A		not specified	Uncertain significance (Mar 25, 2024)
17-19386775-C-T		not specified	Uncertain significance (Jun 16, 2022)
17-19386819-A-G		not specified	Uncertain significance (Jan 23, 2023)
17-19386828-G-C		not specified	Uncertain significance (Oct 05, 2021)
17-19387047-C-G		not specified	Uncertain significance (Feb 13, 2024)
17-19387048-A-G		not specified	Uncertain significance (Mar 24, 2023)
17-19387057-C-A		not specified	Uncertain significance (Dec 21, 2022)
17-19387075-C-T		not specified	Uncertain significance (Oct 20, 2023)
17-19387100-G-A		not specified	Uncertain significance (Mar 29, 2023)
17-19387109-G-C		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFAP4	protein_coding	protein_coding	ENST00000395592	6	3799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.114	0.881	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	117	166	0.705	0.0000100	1802
Missense in Polyphen		53	68.658	0.77194		715
Synonymous	-0.265	76	73.1	1.04	0.00000478	541
Loss of Function	2.43	4	13.7	0.291	6.32e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000941	0.000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved in calcium-dependent cell adhesion or intercellular interactions. May contribute to the elastic fiber assembly and/or maintenance (PubMed:26601954). {ECO:0000269|PubMed:26601954}.
• Pathway: Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.340
• hipred: Y
• hipred_score: 0.580
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0622

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfap4
• Phenotype: respiratory system phenotype

Gene ontology

• Biological process: cell adhesion;UV protection;regulation of collagen metabolic process;elastic fiber assembly;cellular response to UV-B;supramolecular fiber organization
• Cellular component: microfibril;extracellular region;collagen-containing extracellular matrix;elastic fiber
• Molecular function: extracellular matrix structural constituent;protein binding