MNMIP1

Summary

MNMIP1 (manchette microtubule inner protein 1, HGNC:26236) is a protein-coding gene on chromosome 1p34.3, encoding SH3 domain-containing protein 21 (A4FU49).

Predicted to be involved in actin filament organization and cell migration.

Source: NCBI Gene 79729 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 150 total
• MANE Select transcript: NM_001162530

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26236
Approved symbol	MNMIP1
Name	manchette microtubule inner protein 1
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22938
Ensembl gene	ENSG00000214193
Ensembl biotype	protein_coding
Entrez	79729

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 4 protein_coding_CDS_not_defined, 3 protein_coding, 3 nonsense_mediated_decay

ENST00000373137, ENST00000453908, ENST00000474766, ENST00000480549, ENST00000496636, ENST00000505871, ENST00000508854, ENST00000672313, ENST00000672976, ENST00000850902

RefSeq mRNA: 2 — MANE Select: NM_001162530 NM_001162530, NM_024676

CCDS: CCDS30674

Canonical transcript exons

ENST00000453908 — 16 exons

Exon	Start	End
ENSE00001772139	36306368	36306424
ENSE00003459991	36307517	36307607
ENSE00003472936	36306598	36306755
ENSE00003480491	36308389	36308475
ENSE00003491497	36320915	36320978
ENSE00003509323	36319260	36319312
ENSE00003520730	36306842	36306905
ENSE00003543092	36307167	36307285
ENSE00003575218	36319442	36319536
ENSE00003588264	36319071	36319164
ENSE00003590297	36309548	36309590
ENSE00003611049	36307770	36307825
ENSE00003639142	36308109	36308209
ENSE00003661856	36307918	36307963
ENSE00003685676	36319675	36320798
ENSE00003895459	36321056	36321347

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 96.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.8417 / max 195.1644, expressed in 1537 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2181	6.6425	1462
2180	2.4619	601
2179	0.4062	222
2182	0.1653	37
201466	0.1279	36
2183	0.0207	7
2178	0.0171	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of thyroid gland	UBERON:0001119	96.29	gold quality
left lobe of thyroid gland	UBERON:0001120	95.76	gold quality
thyroid gland	UBERON:0002046	93.89	gold quality
skin of leg	UBERON:0001511	93.40	gold quality
skin of abdomen	UBERON:0001416	92.89	gold quality
minor salivary gland	UBERON:0001830	91.82	gold quality
lower esophagus mucosa	UBERON:0035834	91.54	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.66	gold quality
saliva-secreting gland	UBERON:0001044	90.49	gold quality
cerebellar hemisphere	UBERON:0002245	90.10	gold quality
cerebellar cortex	UBERON:0002129	89.94	gold quality
mouth mucosa	UBERON:0003729	89.77	gold quality
parotid gland	UBERON:0001831	89.33	silver quality
zone of skin	UBERON:0000014	89.28	gold quality
left ovary	UBERON:0002119	89.25	gold quality
right frontal lobe	UBERON:0002810	89.15	gold quality
cerebellum	UBERON:0002037	88.01	gold quality
right ovary	UBERON:0002118	87.72	gold quality
sperm	CL:0000019	87.19	gold quality
vena cava	UBERON:0004087	86.88	silver quality
tendon of biceps brachii	UBERON:0008188	86.83	gold quality
ectocervix	UBERON:0012249	86.04	gold quality
male germ cell	CL:0000015	85.75	gold quality
metanephros cortex	UBERON:0010533	85.58	gold quality
anterior cingulate cortex	UBERON:0009835	85.19	gold quality
cingulate cortex	UBERON:0003027	85.14	gold quality
cerebellar vermis	UBERON:0004720	84.29	gold quality
endocervix	UBERON:0000458	84.20	gold quality
esophagus mucosa	UBERON:0002469	84.06	gold quality
nucleus accumbens	UBERON:0001882	83.84	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.04
E-CURD-112	no	2.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting MNMIP1, 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-186-3P	99.51	66.24	1685
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-6827-5P	98.46	64.88	1256
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-6726-5P	95.97	63.72	841
HSA-MIR-920	95.97	63.95	811
HSA-MIR-4435	95.90	65.47	1201
HSA-MIR-4300	95.85	64.56	1003
HSA-MIR-5591-5P	95.85	64.76	1002
HSA-MIR-6090	91.01	62.65	222

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	sh3d21	ENSDARG00000099448
mus_musculus	Sh3d21	ENSMUSG00000073758
rattus_norvegicus	Sh3d21	ENSRNOG00000024566
drosophila_melanogaster	cindr	FBGN0027598
caenorhabditis_elegans	cdap-2	WBGENE00021549

Paralogs (3): SH3KBP1 (ENSG00000147010), NOSTRIN (ENSG00000163072), CD2AP (ENSG00000198087)

Protein

Protein identifiers

SH3 domain-containing protein 21 — A4FU49 (reviewed: A4FU49)

All UniProt accessions (4): A0A5F9ZH69, A0A5F9ZHZ4, A4FU49, D6RD64

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. Gene prediction based on EST data and similarity to mouse and macaca fascicularis orthologs. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (5)

UniProt ID	Names	Canonical?
A4FU49-1	1	yes
A4FU49-3	2
A4FU49-4	3
A4FU49-5	4
A4FU49-6	5

RefSeq proteins (2): NP_001156002, NP_078952 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001452	SH3_domain	Domain
IPR035468	SH3D21_SH3	Domain
IPR036028	SH3-like_dom_sf	Homologous_superfamily
IPR050384	Endophilin_SH3RF	Family

Pfam: PF07653

UniProt features (26 total): splice variant 7, compositionally biased region 6, region of interest 4, sequence conflict 4, sequence variant 2, chain 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4FU49-F1	53.21	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): RRAGTTGT_UNKNOWN, GOBP_ACTIN_FILAMENT_ORGANIZATION, chr1p34, TGANTCA_AP1_C, AACTTT_UNKNOWN, HAMAI_APOPTOSIS_VIA_TRAIL_DN, AGCTCCT_MIR28, NUYTTEN_EZH2_TARGETS_DN, WGTTNNNNNAAA_UNKNOWN, GGGGCCC_MIR296, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, HATADA_METHYLATED_IN_LUNG_CANCER_UP, BRUINS_UVC_RESPONSE_LATE, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12, GOBP_SUPRAMOLECULAR_FIBER_ORGANIZATION

GO Biological Process (2): actin filament organization (GO:0007015), cell migration (GO:0016477)

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
actin cytoskeleton organization	1
supramolecular fiber organization	1
cell motility	1
binding	1

Protein interactions and networks

STRING

634 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MNMIP1	BEND7	Q8N7W2	524
MNMIP1	SHISA4	Q96DD7	511
MNMIP1	LRRC40	Q9H9A6	503
MNMIP1	NAIF1	Q69YI7	485
MNMIP1	LCTL	Q6UWM7	479
MNMIP1	EVA1B	Q9NVM1	477
MNMIP1	ZC3H8	Q8N5P1	470
MNMIP1	SMIM12	Q96EX1	457
MNMIP1	MOCS1	Q9NZB8	452
MNMIP1	SNAPC3	Q92966	451
MNMIP1	LEPROTL1	O95214	451
MNMIP1	KLHL15	Q96M94	449
MNMIP1	NABP2	Q9BQ15	445
MNMIP1	PAMR1	Q6UXH9	412
MNMIP1	ANKRD23	Q86SG2	404
MNMIP1	PHF7	Q9BWX1	404

IntAct

7 interactions, top by confidence:

A	B	Type	Score
SH3D21	EGFR	psi-mi:“MI:0915”(physical association)	0.550
ADAM10	SH3D21	psi-mi:“MI:0407”(direct interaction)	0.440
YAP1	SH3D21	psi-mi:“MI:0407”(direct interaction)	0.440
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (5): SH3D21 (Affinity Capture-MS), SH3D21 (Affinity Capture-MS), SH3D21 (Protein-peptide), FOXRED1 (Cross-Linking-MS (XL-MS)), SH3D21 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GTH6, A0A1B0GUW6, A0A1D5RMD1, A2AQH4, A4FU49, A6NJ88, C4P6S0, D3YU32, E9PAV3, F1QU13, I3L273, J3KML8, P70670, Q32L62, Q3V0E1, Q3V3Q4, Q4R729, Q5H9F3, Q5QJ38, Q5SWP3, Q5U4C1, Q5VWK0, Q5VYM1, Q68DN1, Q6AZ54, Q7TSG5, Q810T2, Q8CH19, Q8K4E0, Q8N3K9, Q8N5Q1, Q8NDH2, Q8TCU4, Q8WNU4, Q8WWL7, Q920R4, Q921B4, Q923B3, Q96JA4, Q96M34

Diamond homologs: A0A8I3PDQ1, A1CEK6, A1DFN5, A2QW93, A4FU49, A4RF61, A7A261, O13736, O35177, O35179, O35964, O42287, O43281, P29355, P34109, P38753, P43603, P56945, Q08012, Q0CJU8, Q0P5B1, Q0U6X7, Q14511, Q15811, Q16584, Q1E878, Q2GT05, Q4R729, Q4WHP5, Q557J6, Q5BBL4, Q5I1X5, Q61140, Q62419, Q62420, Q63767, Q64355, Q66HA1, Q6BNP6, Q6C2N2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	124
Likely benign	16
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2573 predictions. Top by Δscore:

Variant	Effect	Δscore
1:36307282:GGAG:G	donor_gain	1.0000
1:36307283:GAGG:G	donor_gain	1.0000
1:36307285:GGTGA:G	donor_loss	1.0000
1:36307286:GTGAG:G	donor_loss	1.0000
1:36307608:G:GG	donor_gain	1.0000
1:36307916:A:AG	acceptor_gain	1.0000
1:36307917:G:GG	acceptor_gain	1.0000
1:36308387:A:AG	acceptor_gain	1.0000
1:36308388:G:GG	acceptor_gain	1.0000
1:36308476:G:GG	donor_gain	1.0000
1:36309540:C:CA	acceptor_gain	1.0000
1:36309546:A:AG	acceptor_gain	1.0000
1:36309547:G:GG	acceptor_gain	1.0000
1:36320785:G:GT	donor_gain	1.0000
1:36320799:G:GG	donor_gain	1.0000
1:36306751:TGCAG:T	donor_loss	0.9900
1:36306754:AG:A	donor_loss	0.9900
1:36306755:GG:G	donor_loss	0.9900
1:36306756:GTGAG:G	donor_loss	0.9900
1:36306757:T:G	donor_loss	0.9900
1:36306905:GGTG:G	donor_loss	0.9900
1:36306906:G:T	donor_loss	0.9900
1:36306907:T:G	donor_loss	0.9900
1:36307161:TGCTA:T	acceptor_loss	0.9900
1:36307164:TA:T	acceptor_loss	0.9900
1:36307165:A:AT	acceptor_loss	0.9900
1:36307283:G:T	donor_gain	0.9900
1:36307595:A:AG	donor_gain	0.9900
1:36307596:G:GG	donor_gain	0.9900
1:36307627:ACCCT:A	donor_gain	0.9900

AlphaMissense

4884 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000004463 (1:36306432 C>T), RS1000056539 (1:36327299 G>A,T), RS1000294102 (1:36314678 A>G,T), RS1000297447 (1:36322118 C>A,G,T), RS1000429875 (1:36321480 C>A,T), RS1000478263 (1:36305818 G>T), RS1000509514 (1:36305585 C>T), RS1000605516 (1:36305165 C>T), RS1000702607 (1:36317356 C>G), RS1000731433 (1:36310190 G>A), RS1000817431 (1:36317010 T>G), RS1000914577 (1:36304981 G>A), RS1000965000 (1:36322797 A>G), RS1001068633 (1:36328665 A>G), RS1001096147 (1:36310976 T>C)

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

4 associations (top):

Study	Trait	p-value
GCST009391_1405	Metabolite levels	4.000000e-06
GCST90002387_194	Immature fraction of reticulocytes	1.000000e-09
GCST90002400_24	Plateletcrit	4.000000e-12
GCST90002402_540	Platelet count	8.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005132	5-HIAA measurement
EFO:0007985	platelet crit
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, affects methylation, increases abundance	2
Benzo(a)pyrene	affects methylation, decreases methylation	2
FR900359	increases phosphorylation	1
sotorasib	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	decreases reaction, affects binding	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
aflatoxin B2	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
licochalcone B	increases expression	1
bisphenol S	decreases expression	1
jinfukang	increases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Caffeine	affects phosphorylation	1
Calcitriol	increases expression, affects cotreatment	1
Estradiol	affects cotreatment, decreases expression	1
Nitrogen Oxides	affects methylation, increases abundance	1
Oxygen	increases expression	1
Ozone	increases abundance, affects expression	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Testosterone	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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