MFAP3

Summary

MFAP3 (microfibril associated protein 3, HGNC:7034) is a protein-coding gene on chromosome 5q33.2, encoding Microfibril-associated glycoprotein 3 (P55082). Component of the elastin-associated microfibrils.

Predicted to be located in extracellular region.

Source: NCBI Gene 4238 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 58 total
• MANE Select transcript: NM_005927

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7034
Approved symbol	MFAP3
Name	microfibril associated protein 3
Location	5q33.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000037749
Ensembl biotype	protein_coding
OMIM	600491
Entrez	4238

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 7 protein_coding, 6 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay

ENST00000322602, ENST00000439768, ENST00000518497, ENST00000519325, ENST00000519612, ENST00000519928, ENST00000520327, ENST00000520899, ENST00000521527, ENST00000522177, ENST00000522440, ENST00000522782, ENST00000679729, ENST00000681641, ENST00000856253, ENST00000856254

RefSeq mRNA: 3 — MANE Select: NM_005927 NM_001135037, NM_001242336, NM_005927

CCDS: CCDS4324, CCDS47319

Canonical transcript exons

ENST00000522782 — 3 exons

Exon	Start	End
ENSE00000841318	154049557	154050017
ENSE00002097597	154052920	154057450
ENSE00002129467	154038967	154039011

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 92.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.2639 / max 186.5970, expressed in 1786 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
59716	13.9136	1783
59717	0.3502	161

Top tissues by expression

281 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	92.52	gold quality
cortical plate	UBERON:0005343	92.01	gold quality
islet of Langerhans	UBERON:0000006	90.07	gold quality
stromal cell of endometrium	CL:0002255	87.82	gold quality
gall bladder	UBERON:0002110	87.72	gold quality
calcaneal tendon	UBERON:0003701	86.70	gold quality
rectum	UBERON:0001052	86.68	gold quality
smooth muscle tissue	UBERON:0001135	86.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.49	gold quality
tendon	UBERON:0000043	84.65	gold quality
ganglionic eminence	UBERON:0004023	84.63	gold quality
monocyte	CL:0000576	83.90	gold quality
mononuclear cell	CL:0000842	83.75	gold quality
leukocyte	CL:0000738	83.65	gold quality
omental fat pad	UBERON:0010414	83.64	gold quality
peritoneum	UBERON:0002358	83.60	gold quality
tendon of biceps brachii	UBERON:0008188	82.90	silver quality
lymph node	UBERON:0000029	82.52	gold quality
muscle of leg	UBERON:0001383	82.52	gold quality
gastrocnemius	UBERON:0001388	82.43	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.19	gold quality
ventricular zone	UBERON:0003053	81.65	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.42	gold quality
colonic epithelium	UBERON:0000397	81.14	gold quality
heart left ventricle	UBERON:0002084	81.00	gold quality
right atrium auricular region	UBERON:0006631	80.90	gold quality
cardiac ventricle	UBERON:0002082	80.68	gold quality
subcutaneous adipose tissue	UBERON:0002190	80.59	gold quality
heart	UBERON:0000948	80.54	gold quality
vermiform appendix	UBERON:0001154	80.27	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

154 targeting MFAP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-548AE-3P	99.93	72.66	4867

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mfap3	ENSMUSG00000020522
rattus_norvegicus	Mfap3	ENSRNOG00000002443

Paralogs (1): MFAP3L (ENSG00000198948)

Protein

Protein identifiers

Microfibril-associated glycoprotein 3 — P55082 (reviewed: P55082)

All UniProt accessions (6): A0A7P0TA61, A0A7P0TB88, E5RH26, E5RHQ6, E5RJ59, P55082

UniProt curated annotations — full annotation on UniProt →

Function. Component of the elastin-associated microfibrils.

Subcellular location. Cell membrane.

Post-translational modifications. Glycosylated.

Isoforms (2)

UniProt ID	Names	Canonical?
P55082-1	1	yes
P55082-2	2

RefSeq proteins (3): NP_001128509, NP_001229265, NP_005918* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013151	Immunoglobulin_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF00047

UniProt features (15 total): glycosylation site 3, topological domain 2, region of interest 2, signal peptide 1, chain 1, disulfide bond 1, splice variant 1, sequence variant 1, transmembrane region 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P55082-F1	62.00	0.09

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 73–124

Glycosylation sites (3): 41, 110, 36

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-2129379	Molecules associated with elastic fibres
R-HSA-1474244	Extracellular matrix organization
R-HSA-1566948	Elastic fibre formation

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): extracellular region (GO:0005576), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Elastic fibre formation	1
Extracellular matrix organization	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

506 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MFAP3	MFAP2	P55001	889
MFAP3	MFAP1	P55081	870
MFAP3	FBN2	P35556	716
MFAP3	ELN	P15502	675
MFAP3	FBN1	P35555	585
MFAP3	FAM114A2	Q9NRY5	575
MFAP3	MORN4	Q8NDC4	536
MFAP3	ABHD13	Q7L211	524
MFAP3	GALNT10	Q86SR1	505
MFAP3	LOX	P28300	491
MFAP3	COMMD9	Q9P000	489
MFAP3	NOL6	Q9H6R4	460
MFAP3	TMEM212	A6NML5	397
MFAP3	BCL2L12	Q9HB09	368
MFAP3	CCDC190	Q86UF4	351

IntAct

106 interactions, top by confidence:

A	B	Type	Score
TNFSF13B	IPO8	psi-mi:“MI:0914”(association)	0.640
SLC20A1	LIN7A	psi-mi:“MI:0914”(association)	0.640
COMMD6	VPS26C	psi-mi:“MI:0914”(association)	0.640
MFAP3	GRIP1	psi-mi:“MI:0915”(physical association)	0.560
TMEM30B	KLRG2	psi-mi:“MI:0914”(association)	0.530
FAM171B	FAM171A2	psi-mi:“MI:0914”(association)	0.530
MCOLN3	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
PTGER3	PIK3R2	psi-mi:“MI:0914”(association)	0.530
TGFBR2	PIK3R2	psi-mi:“MI:0914”(association)	0.530
SYT12	B4GALT5	psi-mi:“MI:0914”(association)	0.530
ZACN	GPAA1	psi-mi:“MI:0914”(association)	0.530
MRAP2	GOLIM4	psi-mi:“MI:0914”(association)	0.530
LGALS3	PODXL	psi-mi:“MI:0914”(association)	0.530
LRRC8B	SLC25A17	psi-mi:“MI:0914”(association)	0.530
CHRND	TPST2	psi-mi:“MI:0914”(association)	0.530
PTGIR	TMEM63A	psi-mi:“MI:0914”(association)	0.530
CHRNA3	TMEM223	psi-mi:“MI:0914”(association)	0.350
ERGIC3	TMEM223	psi-mi:“MI:0914”(association)	0.350
LGALS8	SLC22A23	psi-mi:“MI:0914”(association)	0.350
BTNL8	TMEM131L	psi-mi:“MI:0914”(association)	0.350
TNFRSF10A	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
SFTPC	CBX6	psi-mi:“MI:0914”(association)	0.350
LGALS9	PODXL	psi-mi:“MI:0914”(association)	0.350

BioGRID (119): MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Affinity Capture-MS), MFAP3 (Proximity Label-MS)

ESM2 similar proteins: A0A0F7YYX3, A1Z0Q5, E1BRC3, E2AX35, E9PVB5, F5HFJ7, O76061, O88452, O97561, P03172, P06476, P09259, P09728, P22484, P24872, P28967, P28981, P32514, P33802, P36318, P55082, P57083, P68327, P84393, P85831, Q05059, Q2YDM0, Q3TBN1, Q499E0, Q4R6V5, Q5BKX0, Q5PQN2, Q5R9E4, Q5RDR5, Q69091, Q69467, Q6AY76, Q6AYF7, Q6DLD9, Q6NVG5

Diamond homologs: A1KZ92, A2A8L5, A2ASS6, A7MBJ4, B3NS99, B4KPU0, B4P5Q9, D3YXG0, H2KZ60, O01761, O42127, O42414, O75121, O94856, P10586, P11362, P14781, P16092, P18460, P18461, P20241, P21802, P21804, P22607, P34082, P55082, P70232, P97685, P97798, Q04589, Q15746, Q28103, Q4H3K6, Q5DTJ9, Q5R412, Q5R9E4, Q61851, Q62845, Q64604, Q68SN8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 116 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Neurotransmitter receptors and postsynaptic signal transmission	6	7.9×	6e-03

GO biological processes:

GO term	Partners	Fold	FDR
acetylcholine receptor signaling pathway	5	30.0×	2e-04
membrane depolarization	5	24.6×	3e-04
monoatomic ion transmembrane transport	6	12.0×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

58 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1036 predictions. Top by Δscore:

Variant	Effect	Δscore
5:154052916:TCAGG:T	acceptor_loss	1.0000
5:154052917:CAGG:C	acceptor_loss	1.0000
5:154052918:A:AG	acceptor_gain	1.0000
5:154052918:AGGT:A	acceptor_gain	1.0000
5:154052919:G:GA	acceptor_loss	1.0000
5:154052919:G:GG	acceptor_gain	1.0000
5:154052919:GGTG:G	acceptor_gain	1.0000
5:154052902:T:G	acceptor_gain	0.9900
5:154052906:T:A	acceptor_gain	0.9900
5:154052911:A:AG	acceptor_gain	0.9900
5:154052912:A:G	acceptor_gain	0.9900
5:154052916:T:G	acceptor_gain	0.9900
5:154052919:GGT:G	acceptor_gain	0.9900
5:154191023:CAGGT:C	donor_loss	0.9900
5:154191024:AGGTG:A	donor_loss	0.9900
5:154191026:GT:G	donor_loss	0.9900
5:154191027:T:A	donor_loss	0.9900
5:154216177:G:GT	donor_gain	0.9900
5:154050013:CAGAG:C	donor_loss	0.9800
5:154050014:AGAGG:A	donor_loss	0.9800
5:154050015:GAGGT:G	donor_loss	0.9800
5:154050016:AGGT:A	donor_loss	0.9800
5:154050017:GGTAA:G	donor_loss	0.9800
5:154050018:G:GC	donor_loss	0.9800
5:154050019:T:G	donor_loss	0.9800
5:154052901:A:AG	acceptor_gain	0.9800
5:154052913:T:G	acceptor_gain	0.9800
5:154052918:AGGTG:A	acceptor_gain	0.9800
5:154052919:GGTGG:G	acceptor_gain	0.9800
5:154191026:G:GG	donor_gain	0.9800

AlphaMissense

805 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:154049939:T:C	C73R	0.995
5:154049977:G:C	W85C	0.995
5:154049977:G:T	W85C	0.995
5:154052980:G:C	R119P	0.995
5:154052988:T:G	Y122D	0.995
5:154049939:T:A	C73S	0.994
5:154049940:G:C	C73S	0.994
5:154052950:T:C	L109P	0.994
5:154049975:T:A	W85R	0.993
5:154049975:T:C	W85R	0.993
5:154052982:G:T	G120W	0.993
5:154049941:T:G	C73W	0.991
5:154052970:T:C	F116L	0.990
5:154052972:T:A	F116L	0.990
5:154052972:T:G	F116L	0.990
5:154052982:G:A	G120R	0.990
5:154052982:G:C	G120R	0.990
5:154052956:T:C	I111T	0.989
5:154052983:G:A	G120E	0.988
5:154052989:A:C	Y122S	0.988
5:154052971:T:G	F116C	0.987
5:154052983:G:T	G120V	0.986
5:154052956:T:G	I111S	0.985
5:154049976:G:C	W85S	0.983
5:154052950:T:A	L109Q	0.982
5:154052988:T:A	Y122N	0.982
5:154052989:A:G	Y122C	0.981
5:154052977:A:T	D118V	0.980
5:154049940:G:A	C73Y	0.979
5:154052977:A:C	D118A	0.976

dbSNP variants (sampled 300 via entrez): RS1000295052 (5:154037560 G>A), RS1000308213 (5:154057076 G>A), RS1000320545 (5:154050085 G>A,C), RS1000411913 (5:154037435 T>C), RS1000892272 (5:154044586 G>A), RS1000893572 (5:154043668 T>G), RS1000916558 (5:154049147 A>G), RS1001007069 (5:154039048 C>CAGTA), RS1001032543 (5:154048832 T>C), RS1001069324 (5:154055697 C>T), RS1001188672 (5:154040563 C>T), RS1001244853 (5:154047502 G>A), RS1001263134 (5:154041977 G>A), RS1001430771 (5:154054010 C>T), RS1001499114 (5:154055335 A>G)

Disease associations

OMIM: gene MIM:600491 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001125_2	Body mass index	6.000000e-06
GCST005830_43	Hand grip strength	4.000000e-08
GCST008830_17	Neurofibrillary tangles	1.000000e-06
GCST010988_346	Adult body size	2.000000e-11
GCST010989_256	Body size at age 10	2.000000e-21
GCST90002409_21	Childhood body mass index	4.000000e-07

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0006941	grip strength measurement
EFO:0006797	neurofibrillary tangles measurement
EFO:0009819	comparative body size at age 10, self-reported

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
tamibarotene	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Cadmium	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Vitallium	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.