MISP3

Summary

MISP3 (MISP family member 3, HGNC:26963) is a protein-coding gene on chromosome 19p13.12, encoding Uncharacterized protein MISP3 (Q96FF7).

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001291291

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26963
Approved symbol	MISP3
Name	MISP family member 3
Location	19p13.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000141854
Ensembl biotype	protein_coding
Entrez	113230

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000269720, ENST00000587086, ENST00000590772, ENST00000591982, ENST00000944820

RefSeq mRNA: 2 — MANE Select: NM_001291291 NM_001291291, NM_001393577

CCDS: CCDS77246

Canonical transcript exons

ENST00000587086 — 3 exons

Exon	Start	End
ENSE00000951089	14074390	14074463
ENSE00002788027	14074706	14075062
ENSE00002972492	14072786	14073877

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 92.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.8022 / max 108.5483, expressed in 1315 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174217	1.9036	738
174213	1.8288	335
174215	1.4734	656
174216	0.4162	218
174214	0.1802	101

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.80	gold quality
mucosa of transverse colon	UBERON:0004991	92.09	gold quality
adult mammalian kidney	UBERON:0000082	87.32	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.81	gold quality
cerebellar hemisphere	UBERON:0002245	86.61	gold quality
cerebellum	UBERON:0002037	86.50	gold quality
cerebellar cortex	UBERON:0002129	86.49	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.48	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	86.36	gold quality
anterior cingulate cortex	UBERON:0009835	86.23	gold quality
hypothalamus	UBERON:0001898	85.70	gold quality
right frontal lobe	UBERON:0002810	85.65	gold quality
temporal lobe	UBERON:0001871	85.48	gold quality
amygdala	UBERON:0001876	85.48	gold quality
prefrontal cortex	UBERON:0000451	85.47	gold quality
apex of heart	UBERON:0002098	85.45	gold quality
Ammon’s horn	UBERON:0001954	85.40	gold quality
cerebral cortex	UBERON:0000956	85.26	gold quality
frontal cortex	UBERON:0001870	85.24	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.83	gold quality
substantia nigra	UBERON:0002038	84.46	gold quality
primary visual cortex	UBERON:0002436	84.09	gold quality
metanephros cortex	UBERON:0010533	83.91	gold quality
right uterine tube	UBERON:0001302	83.85	gold quality
putamen	UBERON:0001874	83.81	gold quality
brain	UBERON:0000955	83.19	gold quality
duodenum	UBERON:0002114	82.99	gold quality
body of stomach	UBERON:0001161	82.78	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	82.76	gold quality
caudate nucleus	UBERON:0001873	82.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting MISP3, 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-6748-5P	100.00	65.81	1057
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-3188	98.58	65.60	878
HSA-MIR-6887-5P	98.56	68.49	1295
HSA-MIR-6795-5P	98.52	68.51	1277
HSA-MIR-6780A-3P	98.42	67.49	1518
HSA-MIR-653-3P	98.31	67.71	1542
HSA-MIR-6511A-5P	98.13	67.47	1770
HSA-MIR-4665-5P	97.91	67.69	1536
HSA-MIR-5000-5P	97.40	66.11	1055
HSA-MIR-25-5P	87.02	64.95	84

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	misp3	ENSDARG00000090793
mus_musculus	Misp3	ENSMUSG00000074217
rattus_norvegicus	Misp3	ENSRNOG00000005619

Paralogs (1): MISP (ENSG00000099812)

Protein

Protein identifiers

Uncharacterized protein MISP3 — Q96FF7 (reviewed: Q96FF7)

Alternative names: MISP family member 3

All UniProt accessions (3): A0A044PY82, Q96FF7, K7ELQ6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the MISP family.

RefSeq proteins (2): NP_001278220, NP_001380506 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029304	AKAP2_C	Domain
IPR042779	MISP/MISP3-like	Family

Pfam: PF15304

UniProt features (6 total): compositionally biased region 3, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96FF7-F1	71.32	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): chr19p13, YOSHIMURA_MAPK8_TARGETS_UP, HES2_TARGET_GENES, PCGF1_TARGET_GENES, ZNF322_TARGET_GENES, ZNF423_TARGET_GENES, HAY_BONE_MARROW_PLATELET, DESCARTES_MAIN_FETAL_PARIETAL_AND_CHIEF_CELLS, DESCARTES_FETAL_PLACENTA_TROPHOBLAST_GIANT_CELLS, BDP1_TARGET_GENES, PSIP1_TARGET_GENES, TRAVAGLINI_LUNG_PROXIMAL_CILIATED_CELL, TRAVAGLINI_LUNG_PLATELET_MEGAKARYOCYTE_CELL, HE_LIM_SUN_FETAL_LUNG_C1_PULMONARY_NE_PRECURSOR_CELL, ZNF320_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

158 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MISP3	PDZD9	Q8IXQ8	623
MISP3	MISP	Q8IVT2	599
MISP3	CLDND2	Q8NHS1	592
MISP3	TMCO6	Q96DC7	582
MISP3	PALM2AKAP2	Q9Y2D5	500
MISP3	IFITM10	A6NMD0	374
MISP3	APOL6	Q9BWW8	373
MISP3	TENM4	Q6N022	371
MISP3	J3KSM2	J3KSM2	352
MISP3	CAVIN4	Q5BKX8	348
MISP3	PCNT	O95613	325
MISP3	OAZ1	P54368	322
MISP3	FOXD2	O60548	315
MISP3	RRAD	P55042	301
MISP3	PZP	P20742	298

IntAct

2 interactions, top by confidence:

A	B	Type	Score
	PDLIM1	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): LOC113230 (Affinity Capture-MS), LOC113230 (Affinity Capture-MS), LOC113230 (Affinity Capture-MS), LOC113230 (Affinity Capture-MS)

ESM2 similar proteins: A1A5D9, A1L3T7, A4FV37, A6NC98, A6NJZ7, A6NNM3, O15049, P0C7N4, P0CW27, P58660, Q0P5D1, Q1HGE8, Q2NL23, Q3LUD3, Q3UPH7, Q494R4, Q4QRL3, Q5JYT7, Q5ND29, Q5XIS1, Q64697, Q6QZQ4, Q6UXH0, Q6ZS72, Q7Z6P3, Q8BLS7, Q8C2K5, Q8C7U1, Q8CB62, Q8CB87, Q8CHW5, Q8N137, Q8R1L8, Q8TE77, Q8TER5, Q91VJ2, Q969G5, Q96EN9, Q96FF7, Q96LX7

Diamond homologs: Q5RBH3, Q8IVT2, Q96FF7, Q9D279

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

301 predictions. Top by Δscore:

Variant	Effect	Δscore
19:14073874:ACCGG:A	donor_loss	0.8600
19:14073875:CCGGT:C	donor_loss	0.8600
19:14073876:CGG:C	donor_loss	0.8600
19:14073877:GGTAA:G	donor_loss	0.8600
19:14073879:TAA:T	donor_loss	0.8600
19:14073880:AAGCC:A	donor_loss	0.8400
19:14073856:GAGCC:G	donor_gain	0.8200
19:14074388:A:AG	acceptor_gain	0.8100
19:14074389:G:GG	acceptor_gain	0.8100
19:14073878:G:GG	donor_gain	0.7700
19:14074389:GC:G	acceptor_gain	0.7500
19:14074888:A:AG	acceptor_gain	0.7500
19:14074889:G:GG	acceptor_gain	0.7500
19:14074389:GCGA:G	acceptor_gain	0.7000
19:14074322:A:C	acceptor_gain	0.6600
19:14073881:AGCCG:A	donor_loss	0.6500
19:14074322:AAGG:A	acceptor_gain	0.6400
19:14073875:CCG:C	donor_gain	0.6200
19:14074323:AGG:A	acceptor_gain	0.6200
19:14074324:GGG:G	acceptor_gain	0.6200
19:14074384:CCGCA:C	acceptor_loss	0.5700
19:14074385:CGCA:C	acceptor_loss	0.5700
19:14074386:GCAGC:G	acceptor_loss	0.5700
19:14074388:AG:A	acceptor_loss	0.5700
19:14074389:G:A	acceptor_loss	0.5700
19:14074465:TGG:T	donor_gain	0.5600
19:14074466:GGG:G	donor_gain	0.5600
19:14074347:T:TA	acceptor_gain	0.5500
19:14074376:CCCTT:C	acceptor_loss	0.5500
19:14074377:CCTTC:C	acceptor_loss	0.5500

AlphaMissense

1367 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:14073335:T:C	I9T	0.993
19:14073323:T:A	I5N	0.992
19:14073503:T:C	M65T	0.989
19:14073335:T:G	I9S	0.984
19:14073329:G:C	R7P	0.974
19:14073331:G:A	E8K	0.972
19:14073352:C:A	R15S	0.970
19:14073332:A:T	E8V	0.969
19:14074422:T:A	W201R	0.968
19:14074422:T:C	W201R	0.968
19:14073335:T:A	I9N	0.967
19:14073616:T:C	F103L	0.967
19:14073618:C:A	F103L	0.967
19:14073618:C:G	F103L	0.967
19:14074424:G:C	W201C	0.966
19:14074424:G:T	W201C	0.966
19:14073338:G:C	R10P	0.965
19:14073323:T:G	I5S	0.962
19:14073343:A:C	S12R	0.960
19:14073345:C:A	S12R	0.960
19:14073345:C:G	S12R	0.960
19:14073504:G:A	M65I	0.958
19:14073504:G:C	M65I	0.958
19:14073504:G:T	M65I	0.958
19:14073357:G:C	E16D	0.957
19:14073357:G:T	E16D	0.957
19:14073353:G:C	R15P	0.956
19:14073609:G:C	K100N	0.954
19:14073609:G:T	K100N	0.954
19:14073367:C:A	R20S	0.949

dbSNP variants (sampled 300 via entrez): RS1000420910 (19:14074327 G>C), RS1001660788 (19:14075021 C>T), RS1001883145 (19:14074781 CG>C,CGG,CGGGG), RS1003223982 (19:14074177 T>C), RS1003518665 (19:14074439 G>A,T), RS1003973553 (19:14072086 C>G,T), RS1004329387 (19:14073934 T>C), RS1004620750 (19:14073735 G>C,T), RS1004756764 (19:14073206 C>T), RS1005198635 (19:14075047 CTCT>C), RS1005685045 (19:14075420 TAA>T,TA,TAAA), RS1006020137 (19:14071657 C>G), RS1006455993 (19:14071016 G>A), RS1006485393 (19:14071937 C>G,T), RS1007348551 (19:14071099 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, decreases expression	2
beta-lapachone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	increases expression	1
Acrylamide	decreases expression	1
Particulate Matter	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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