MFAP3

microfibril associated protein 3, the group of I-set domain containing

Basic information

Region (hg38): 5:154038958-154220478

Links

ENSG00000037749 ∙ NCBI:4238 ∙ OMIM:600491 ∙ HGNC:7034 ∙ Uniprot:P55082 ∙ 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 MFAP3 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MFAP3 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in MFAP3

This is a list of pathogenic ClinVar variants found in the MFAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-154049736-G-A		not specified	Uncertain significance (Aug 01, 2022)
5-154049889-C-T		not specified	Uncertain significance (Sep 17, 2021)
5-154049894-G-T		not specified	Uncertain significance (Oct 05, 2023)
5-154049900-G-A		not specified	Uncertain significance (Oct 25, 2022)
5-154049903-A-G		not specified	Uncertain significance (Apr 12, 2022)
5-154049927-G-A		not specified	Uncertain significance (Apr 13, 2022)
5-154052989-A-G		not specified	Uncertain significance (Feb 14, 2024)
5-154053015-C-T		not specified	Uncertain significance (Jun 22, 2021)
5-154053016-G-A		not specified	Likely benign (Nov 27, 2023)
5-154053046-T-C		not specified	Uncertain significance (Sep 15, 2022)
5-154053129-C-T		not specified	Uncertain significance (Jun 22, 2021)
5-154053140-G-C		not specified	Uncertain significance (Aug 09, 2021)
5-154053147-A-T		not specified	Uncertain significance (Jun 21, 2021)
5-154053156-C-T		not specified	Uncertain significance (May 05, 2023)
5-154053190-G-A		not specified	Uncertain significance (Nov 13, 2023)
5-154053282-G-T		not specified	Uncertain significance (Aug 15, 2023)
5-154053460-C-T		not specified	Uncertain significance (Aug 09, 2021)
5-154053469-G-A		not specified	Uncertain significance (Dec 03, 2021)
5-154053498-C-T		not specified	Uncertain significance (Dec 20, 2023)
5-154053514-G-A		not specified	Uncertain significance (Oct 13, 2023)
5-154053651-A-G		not specified	Uncertain significance (Dec 18, 2023)
5-154053684-G-A		not specified	Uncertain significance (May 22, 2023)
5-154191000-C-G		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MFAP3	protein_coding	protein_coding	ENST00000436816	2	181573

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00112	0.848	125716	0	23	125739	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	182	203	0.896	0.0000109	2385
Missense in Polyphen		75	101.11	0.74176		1151
Synonymous	-0.855	80	70.8	1.13	0.00000352	718
Loss of Function	1.24	6	10.3	0.584	5.82e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the elastin-associated microfibrils.
• Pathway: Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.425
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.0720
• hipred: N
• hipred_score: 0.325
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mfap3

Gene ontology

• Cellular component: extracellular region;plasma membrane;integral component of membrane