MFAP2

microfibril associated protein 2

Basic information

Region (hg38): 1:16974501-16980632

Links

ENSG00000117122 ∙ NCBI:4237 ∙ OMIM:156790 ∙ HGNC:7033 ∙ Uniprot:P55001 ∙ 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 MFAP2 gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	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)
1-16977172-C-T		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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