MFAP3L

Summary

MFAP3L (microfibril associated protein 3 like, HGNC:29083) is a protein-coding gene on chromosome 4q33, encoding Microfibrillar-associated protein 3-like (O75121). May participate in the nuclear signaling of EGFR and MAPK1/ERK2.

Located in several cellular components, including cell junction; nucleoplasm; and plasma membrane.

Source: NCBI Gene 9848 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_021647

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29083
Approved symbol	MFAP3L
Name	microfibril associated protein 3 like
Location	4q33
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0626, NYD-sp9
Ensembl gene	ENSG00000198948
Ensembl biotype	protein_coding
OMIM	616523
Entrez	9848

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 24 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000361618, ENST00000393702, ENST00000393704, ENST00000502832, ENST00000504999, ENST00000506110, ENST00000506764, ENST00000507601, ENST00000510306, ENST00000512698, ENST00000514683, ENST00000904717, ENST00000904718, ENST00000904719, ENST00000904720, ENST00000932910, ENST00000932911, ENST00000932912, ENST00000932913, ENST00000932914, ENST00000932915, ENST00000932916, ENST00000932917, ENST00000932918, ENST00000960613

RefSeq mRNA: 4 — MANE Select: NM_021647 NM_001009554, NM_001301647, NM_001301648, NM_021647

CCDS: CCDS34103, CCDS43281

Canonical transcript exons

ENST00000361618 — 3 exons

Exon	Start	End
ENSE00001595580	169986602	169992309
ENSE00002066189	170026234	170026395
ENSE00002298034	170005580	170006010

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 99.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.5644 / max 325.6449, expressed in 1161 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
54820	4.6169	965
54819	1.4266	455
54821	0.6497	357
54818	0.3695	176
54825	0.1300	47
54823	0.1218	67
54817	0.0995	4
54824	0.0918	39
54822	0.0584	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.86	gold quality
choroid plexus epithelium	UBERON:0003911	99.16	gold quality
pigmented layer of retina	UBERON:0001782	99.01	gold quality
corpus epididymis	UBERON:0004359	97.89	gold quality
endothelial cell	CL:0000115	97.69	gold quality
cranial nerve II	UBERON:0000941	96.98	gold quality
medial globus pallidus	UBERON:0002477	96.58	gold quality
male germ cell	CL:0000015	96.44	gold quality
globus pallidus	UBERON:0001875	96.44	gold quality
caput epididymis	UBERON:0004358	96.19	gold quality
lateral globus pallidus	UBERON:0002476	95.59	gold quality
corpus callosum	UBERON:0002336	95.45	gold quality
inferior vagus X ganglion	UBERON:0005363	95.40	gold quality
tibia	UBERON:0000979	95.34	gold quality
oocyte	CL:0000023	95.14	gold quality
Brodmann (1909) area 23	UBERON:0013554	95.09	gold quality
CA1 field of hippocampus	UBERON:0003881	95.07	gold quality
nephron tubule	UBERON:0001231	95.05	gold quality
renal medulla	UBERON:0000362	94.70	gold quality
upper leg skin	UBERON:0004262	94.61	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	94.60	gold quality
secondary oocyte	CL:0000655	94.22	gold quality
subthalamic nucleus	UBERON:0001906	94.00	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.84	gold quality
right testis	UBERON:0004534	93.77	gold quality
left testis	UBERON:0004533	93.63	gold quality
medulla oblongata	UBERON:0001896	93.26	gold quality
superior vestibular nucleus	UBERON:0007227	93.10	gold quality
upper arm skin	UBERON:0004263	92.82	gold quality
substantia nigra pars compacta	UBERON:0001965	92.74	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	14.50
E-ANND-3	yes	6.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

236 targeting MFAP3L, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753

Literature-anchored findings (GeneRIF, showing 1)

• MFAP3L activation promotes colorectal cancer cell invasion and metastasis. (PMID:24735981)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mfap3l	ENSDARG00000062752
mus_musculus	Mfap3l	ENSMUSG00000031647
rattus_norvegicus	Mfap3l	ENSRNOG00000011775

Paralogs (1): MFAP3 (ENSG00000037749)

Protein

Protein identifiers

Microfibrillar-associated protein 3-like — O75121 (reviewed: O75121)

Alternative names: Testis development protein NYD-SP9

All UniProt accessions (7): O75121, D6R9L7, D6RAB5, D6RCC0, D6RCF0, D6RDM6, D6RGZ8

UniProt curated annotations — full annotation on UniProt →

Function. May participate in the nuclear signaling of EGFR and MAPK1/ERK2. May a have a role in metastasis.

Subcellular location. Cell membrane. Nucleus. Cytoplasm.

Tissue specificity. Highly expressed in testis.

Isoforms (3)

UniProt ID	Names	Canonical?
O75121-1	1	yes
O75121-2	2
O75121-3	3

RefSeq proteins (4): NP_001009554, NP_001288576, NP_001288577, NP_067679* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF07679

UniProt features (25 total): modified residue 5, glycosylation site 5, splice variant 3, topological domain 2, region of interest 2, compositionally biased region 2, signal peptide 1, chain 1, disulfide bond 1, sequence conflict 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75121-F1	61.86	0.18

Functional residue map

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

Post-translational modifications (5): 287, 298, 303, 306, 307

Disulfide bonds (1): 68–125

Glycosylation sites (5): 33, 37, 67, 111, 135

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 185 (showing top): LEE_NEURAL_CREST_STEM_CELL_DN, DARWICHE_PAPILLOMA_PROGRESSION_RISK, CTATGCA_MIR153, BROWNE_HCMV_INFECTION_12HR_UP, CAIRO_HEPATOBLASTOMA_CLASSES_DN, INGRAM_SHH_TARGETS_UP, CAIRO_HEPATOBLASTOMA_DN, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, GOCC_NEURON_PROJECTION, RIGGINS_TAMOXIFEN_RESISTANCE_DN, chr4q33, PACHER_TARGETS_OF_IGF1_AND_IGF2_UP

GO Biological Process (0):

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

GO Cellular Component (7): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), plasma membrane (GO:0005886), cell junction (GO:0030054), neuron projection (GO:0043005), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

508 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MFAP3L	SFT2D2	O95562	582
MFAP3L	FAM204A	Q9H8W3	528
MFAP3L	NIP7	Q9Y221	479
MFAP3L	MMS22L	Q6ZRQ5	472
MFAP3L	CSPG5	O95196	447
MFAP3L	KCNS1	Q96KK3	447
MFAP3L	AADAT	Q8N5Z0	445
MFAP3L	MBIP	Q9NS73	443
MFAP3L	PALM2AKAP2	Q9Y2D5	432
MFAP3L	ATL2	Q8NHH9	411
MFAP3L	P4HTM	Q9NXG6	406
MFAP3L	NUP155	O75694	392
MFAP3L	PAK1IP1	Q9NWT1	383
MFAP3L	MFAP1	P55081	378
MFAP3L	LINC03041	A6NGG3	374

IntAct

6 interactions, top by confidence:

A	B	Type	Score
KCNE3	RIOK3	psi-mi:“MI:0914”(association)	0.530
CEACAM1	MFAP3L	psi-mi:“MI:0915”(physical association)	0.400
MFAP3L	MPZL2	psi-mi:“MI:0915”(physical association)	0.400
MFAP3L	MXRA5	psi-mi:“MI:0915”(physical association)	0.400
	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): MFAP3L (Affinity Capture-RNA), MFAP3L (Affinity Capture-MS), MFAP3L (Proximity Label-MS), MFAP3L (Proximity Label-MS)

ESM2 similar proteins: A2A9G7, A2RV66, A6NKW6, A6QQ93, A7YDW0, G5EF33, O13980, O55159, O75121, O96838, P09312, P34259, P34292, P34553, P45442, P55082, Q02223, Q03345, Q07FZ2, Q10128, Q14CH0, Q22747, Q29000, Q56A20, Q5R7R7, Q5R9E4, Q5RBY8, Q5RJX2, Q68D42, Q6AYF7, Q6DE06, Q6P995, Q6UWV7, Q6ZN28, Q75QW1, Q77NN6, Q80ZA7, Q86198, Q86516, Q8AXQ3

Diamond homologs: G5EG78, H2KZ60, O75121, P17948, P53767, Q6AYP2, Q9U308, A8WGA3, B0BNK7, D4ABX8, O00533, O42127, O42414, O94856, P11627, P20241, P28693, P29323, P32004, P35331, P35916, P54763, P70232, P82987, P97300, P97685, P97686, Q03696, Q05695, Q1ENI8, Q26474, Q50L44, Q5WRU0, Q6PJG9, Q7TPD3, Q80W87, Q80XU8, Q810U3, Q810U4, Q8BFR2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1286 predictions. Top by Δscore:

Variant	Effect	Δscore
4:169992305:TTTTC:T	acceptor_gain	0.9900
4:169992306:TTTC:T	acceptor_gain	0.9900
4:169992307:TTC:T	acceptor_gain	0.9900
4:169992310:C:CC	acceptor_gain	0.9900
4:169992314:C:CT	acceptor_gain	0.9900
4:170025198:A:AC	donor_gain	0.9900
4:170025199:C:CC	donor_gain	0.9900
4:170025199:CGGT:C	donor_gain	0.9900
4:170026229:CTAA:C	donor_loss	0.9900
4:170026230:TAACC:T	donor_loss	0.9900
4:170026231:AACC:A	donor_loss	0.9900
4:170026232:ACCTG:A	donor_loss	0.9900
4:170026233:C:G	donor_loss	0.9900
4:170026235:TGAC:T	donor_gain	0.9900
4:169992306:TTTCC:T	acceptor_loss	0.9800
4:169992307:TTCC:T	acceptor_loss	0.9800
4:169992308:TC:T	acceptor_gain	0.9800
4:169992308:TCCT:T	acceptor_loss	0.9800
4:169992309:CC:C	acceptor_gain	0.9800
4:169992310:C:A	acceptor_loss	0.9800
4:169992311:T:A	acceptor_loss	0.9800
4:169991469:T:C	donor_gain	0.9700
4:170005581:T:TA	donor_gain	0.9700
4:170006007:GAACC:G	acceptor_loss	0.9700
4:170006008:AACC:A	acceptor_loss	0.9700
4:170006009:ACCTG:A	acceptor_loss	0.9700
4:170006010:CCTG:C	acceptor_loss	0.9700
4:170006011:C:CG	acceptor_loss	0.9700
4:170006012:T:A	acceptor_loss	0.9700
4:170026228:GCTAA:G	donor_loss	0.9700

AlphaMissense

2695 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:169991930:T:A	K226N	1.000
4:169991930:T:G	K226N	1.000
4:169991949:G:T	A220D	1.000
4:169991950:C:G	A220P	1.000
4:169991952:A:G	L219P	1.000
4:169991994:G:T	A205D	1.000
4:169991995:C:G	A205P	1.000
4:169992015:A:G	L198P	1.000
4:169992072:A:G	L179P	1.000
4:169991895:G:T	A238D	0.999
4:169991898:A:G	L237P	0.999
4:169991913:C:G	R232P	0.999
4:169991916:G:T	A231D	0.999
4:169991917:C:G	A231P	0.999
4:169991919:A:G	F230S	0.999
4:169991931:T:A	K226I	0.999
4:169991958:A:G	L217P	0.999
4:169991964:T:A	K215I	0.999
4:169991976:A:T	I211N	0.999
4:169991979:A:G	I210T	0.999
4:169991979:A:T	I210N	0.999
4:169991983:G:A	P209S	0.999
4:169991983:G:T	P209T	0.999
4:169991985:A:C	I208S	0.999
4:169991985:A:G	I208T	0.999
4:169991988:C:G	R207P	0.999
4:169992007:C:G	A201P	0.999
4:169992028:C:A	G194C	0.999
4:169992028:C:G	G194R	0.999
4:169992038:A:C	F190L	0.999

dbSNP variants (sampled 300 via entrez): RS1000033622 (4:170023665 T>G), RS1000064115 (4:170020236 T>C), RS1000086269 (4:169995621 T>TA), RS1000120126 (4:170026134 A>G,T), RS1000142270 (4:169992777 A>G), RS1000342178 (4:170011562 C>G), RS1000396160 (4:170011155 C>G), RS1000522452 (4:169999708 G>A), RS1000571908 (4:169991099 T>C), RS10006800 (4:169990592 C>T), RS1000795237 (4:170000048 G>A), RS1000876333 (4:169988761 T>C), RS1000981155 (4:169995172 A>G), RS1001023494 (4:170005814 C>T), RS1001035914 (4:170022256 C>G)

Disease associations

OMIM: gene MIM:616523 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002696_8	Anxiety disorder	9.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, increases expression, increases methylation, affects cotreatment	8
trichostatin A	affects cotreatment, decreases expression, increases expression	3
Nickel	decreases expression, increases expression	3
methylmercuric chloride	decreases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Estradiol	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
potassium chromate(VI)	increases expression	1
avobenzone	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Vorinostat	affects cotreatment, decreases expression	1
Air Pollutants, Occupational	increases expression	1
Benzo(a)pyrene	increases methylation	1
Ethinyl Estradiol	increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Zinc	decreases expression	1
Isotretinoin	decreases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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