SPMIP9

Summary

SPMIP9 (sperm microtubule inner protein 9, HGNC:26341) is a protein-coding gene on chromosome 2p11.2, encoding Protein SPMIP9 (Q96LM6). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagella axoneme.

Predicted to be involved in flagellated sperm motility. Located in cytoplasm.

Source: NCBI Gene 200523 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_152670

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26341
Approved symbol	SPMIP9
Name	sperm microtubule inner protein 9
Location	2p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25369, TSC21
Ensembl gene	ENSG00000172073
Ensembl biotype	protein_coding
OMIM	619676
Entrez	200523

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000303254

RefSeq mRNA: 1 — MANE Select: NM_152670 NM_152670

CCDS: CCDS2003

Canonical transcript exons

ENST00000303254 — 4 exons

Exon	Start	End
ENSE00001144244	88529052	88529585
ENSE00001144251	88525635	88525671
ENSE00001158393	88526405	88526497
ENSE00001158398	88524649	88524782

Expression profiles

Bgee: expression breadth broad, 25 present calls, max score 95.66.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1371 / max 121.3419, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21348	0.1371	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	95.66	gold quality
left testis	UBERON:0004533	94.58	gold quality
testis	UBERON:0000473	91.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.16	gold quality
pancreatic ductal cell	CL:0002079	87.38	silver quality
sperm	CL:0000019	84.89	silver quality
tibialis anterior	UBERON:0001385	83.26	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.59	gold quality
kidney epithelium	UBERON:0004819	80.93	gold quality
ileal mucosa	UBERON:0000331	76.83	silver quality
cardiac muscle of right atrium	UBERON:0003379	74.80	gold quality
left ventricle myocardium	UBERON:0006566	73.63	gold quality
upper arm skin	UBERON:0004263	71.03	gold quality
secondary oocyte	CL:0000655	69.32	silver quality
adult organism	UBERON:0007023	67.84	gold quality
nasal cavity epithelium	UBERON:0005384	66.71	gold quality
deltoid	UBERON:0001476	66.14	gold quality
superficial temporal artery	UBERON:0001614	62.56	gold quality
myocardium	UBERON:0002349	61.71	gold quality
layer of synovial tissue	UBERON:0007616	58.72	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.58	gold quality
pylorus	UBERON:0001166	58.55	gold quality
inferior vagus X ganglion	UBERON:0005363	58.15	gold quality
nipple	UBERON:0002030	58.12	gold quality
quadriceps femoris	UBERON:0001377	57.99	gold quality
pharyngeal mucosa	UBERON:0000355	57.92	gold quality
saphenous vein	UBERON:0007318	57.79	gold quality
pericardium	UBERON:0002407	57.68	silver quality
renal medulla	UBERON:0000362	57.66	gold quality
subthalamic nucleus	UBERON:0001906	57.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

4 targeting SPMIP9, 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-6077	99.99	68.04	2299
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-4793-3P	94.87	65.85	896

Literature-anchored findings (GeneRIF, showing 1)

• Identification of a novel gene, Tsc21, exclusively expressed in testes. (PMID:17091336)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmip9	ENSMUSG00000051896
rattus_norvegicus	Spmip9	ENSRNOG00000006476

Protein

Protein identifiers

Protein SPMIP9 — Q96LM6 (reviewed: Q96LM6)

Alternative names: Sperm microtubule inner protein 9, Testis-expressed sequence 37 protein, Testis-specific conserved protein of 21 kDa

All UniProt accessions (2): Q96LM6, A0A140VK60

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagella axoneme.

Subunit / interactions. Microtubule inner protein component of sperm flagellar doublet microtubules.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Tissue specificity. Testis-specific. Detected in the germ cell lineage at all stages.

RefSeq proteins (1): NP_689883* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029361	SPMIP9	Family

Pfam: PF15217

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LM6-F1	55.32	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): FXR_IR1_Q6, AREB6_03, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, chr2p11, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, TST1_01, MARTENS_TRETINOIN_RESPONSE_UP, GOCC_AXONEMAL_MICROTUBULE, GOCC_9PLUS2_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER

GO Biological Process (1): flagellated sperm motility (GO:0030317)

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

GO Cellular Component (8): nucleus (GO:0005634), cytoplasm (GO:0005737), sperm flagellum (GO:0036126), axonemal A tubule inner sheath (GO:0160111), cytoskeleton (GO:0005856), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
9+2 motile cilium	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

478 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMIP9	TEX44	Q53QW1	667
SPMIP9	TEX36	Q5VZQ5	624
SPMIP9	TEX55	Q96M34	585
SPMIP9	TEX35	Q5T0J7	571
SPMIP9	THNSL2	Q86YJ6	568
SPMIP9	TSC2	P49815	558
SPMIP9	PRSS55	Q6UWB4	539
SPMIP9	FOXI3	A8MTJ6	515
SPMIP9	C5orf52	A6NGY3	507
SPMIP9	CCDC116	Q8IYX3	497
SPMIP9	SMYD1	Q8NB12	481
SPMIP9	PRSS54	Q6PEW0	479
SPMIP9	SPATA31E1	Q6ZUB1	475
SPMIP9	CFAP97D1	B2RV13	474
SPMIP9	LRRC72	A6NJI9	447

IntAct

146 interactions, top by confidence:

A	B	Type	Score
DAZAP2	SPMIP9	psi-mi:“MI:0915”(physical association)	0.780
TRIP13	SPMIP9	psi-mi:“MI:0915”(physical association)	0.780
SPMIP9	DAZAP2	psi-mi:“MI:0915”(physical association)	0.780
SPMIP9	TRIP13	psi-mi:“MI:0915”(physical association)	0.780
RBPMS	SPMIP9	psi-mi:“MI:0915”(physical association)	0.670
SPMIP9	FAM136A	psi-mi:“MI:0915”(physical association)	0.620
KRTAP6-2	SPMIP9	psi-mi:“MI:0915”(physical association)	0.600
SPMIP9	KPNA3	psi-mi:“MI:0915”(physical association)	0.560
KPNA3	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
SPMIP9	CAMK2A	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-2	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
VAC14	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
KRTAP13-2	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
ATXN1L	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
ZBTB32	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
SPMIP9	PITX2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-4	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
SPMIP9	RBFOX1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (54): TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid), TEX37 (Two-hybrid)

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GTJ6, A0A1B0GUX0, A0A3Q1MT14, A0JNL1, A5PJD8, B9EJX3, E1B9R1, E1BNS6, F1MMV1, Q0P591, Q148A4, Q14BB9, Q1JPL0, Q2KJ10, Q2MH31, Q2T9T0, Q2TA11, Q32L72, Q32L77, Q3V0Q6, Q5BN46, Q5PQN4, Q5RBH3, Q5RHU7, Q5SPV6, Q5SVJ3, Q5VTT2, Q5VZQ5, Q66HR9, Q6AYM0, Q7Z5V6, Q8CDU5, Q8N5S3, Q8N865, Q8NA69, Q8NCR6, Q8NEG2, Q95LU0, Q96K30

Diamond homologs: A5PJD8, Q96LM6, Q9DAG4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 45 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
Keratinization	9	21.8×	2e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

526 predictions. Top by Δscore:

Variant	Effect	Δscore
2:88529050:A:AG	acceptor_gain	0.9900
2:88529051:G:GG	acceptor_gain	0.9900
2:88529051:GC:G	acceptor_gain	0.9900
2:88529051:GCA:G	acceptor_gain	0.9900
2:88524727:GCG:G	donor_gain	0.9800
2:88524770:A:T	donor_gain	0.9800
2:88524783:G:GG	donor_gain	0.9800
2:88524794:G:GT	donor_gain	0.9800
2:88524795:G:T	donor_gain	0.9800
2:88526464:G:GT	donor_gain	0.9800
2:88526493:AAGAG:A	donor_loss	0.9800
2:88526494:AGAG:A	donor_loss	0.9800
2:88526495:GAG:G	donor_gain	0.9800
2:88526496:AG:A	donor_loss	0.9800
2:88526497:GG:G	donor_loss	0.9800
2:88526498:GTA:G	donor_loss	0.9800
2:88526507:C:T	donor_gain	0.9800
2:88529046:CCACA:C	acceptor_loss	0.9800
2:88529047:CACAG:C	acceptor_loss	0.9800
2:88529048:ACAG:A	acceptor_loss	0.9800
2:88529049:CA:C	acceptor_loss	0.9800
2:88529050:AGCAG:A	acceptor_gain	0.9800
2:88529051:G:A	acceptor_loss	0.9800
2:88529051:GCAGG:G	acceptor_gain	0.9800
2:88524779:GTCT:G	donor_gain	0.9700
2:88526511:C:T	donor_gain	0.9700
2:88529048:A:AG	acceptor_gain	0.9600
2:88529032:T:G	acceptor_gain	0.9500
2:88529049:C:G	acceptor_gain	0.9400
2:88524776:GCT:G	donor_gain	0.9300

AlphaMissense

1192 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:88529187:T:C	F86L	0.943
2:88529189:C:A	F86L	0.943
2:88529189:C:G	F86L	0.943
2:88529142:T:C	F71L	0.894
2:88529144:C:A	F71L	0.894
2:88529144:C:G	F71L	0.894
2:88529190:T:C	F87L	0.890
2:88529192:C:A	F87L	0.890
2:88529192:C:G	F87L	0.890
2:88529463:T:C	F178L	0.889
2:88529465:T:A	F178L	0.889
2:88529465:T:G	F178L	0.889
2:88526432:A:C	S19R	0.862
2:88526434:C:A	S19R	0.862
2:88526434:C:G	S19R	0.862
2:88529088:T:C	F53L	0.840
2:88529090:T:A	F53L	0.840
2:88529090:T:G	F53L	0.840
2:88529235:T:C	F102L	0.794
2:88529237:C:A	F102L	0.794
2:88529237:C:G	F102L	0.794
2:88529171:C:A	D80E	0.788
2:88529171:C:G	D80E	0.788
2:88529447:G:C	W172C	0.781
2:88529447:G:T	W172C	0.781
2:88529169:G:C	D80H	0.774
2:88529074:T:C	L48P	0.768
2:88529143:T:C	F71S	0.768
2:88529159:G:A	M76I	0.754
2:88529159:G:C	M76I	0.754

dbSNP variants (sampled 300 via entrez): RS1000636536 (2:88525105 C>T), RS1001076160 (2:88527844 A>T), RS1001133342 (2:88528095 TATTA>T), RS1001348610 (2:88523272 TAAA>T), RS1001831470 (2:88525741 G>A,C), RS1001993070 (2:88525407 C>G), RS1002134425 (2:88525539 A>G), RS1002380880 (2:88524436 C>CT), RS1004111116 (2:88523101 T>C), RS1004335257 (2:88527231 G>A), RS1004750927 (2:88523013 C>T), RS1004872822 (2:88524120 C>G,T), RS1005338814 (2:88528610 C>T), RS1005406619 (2:88524709 C>A), RS1005491849 (2:88523270 C>T)

Disease associations

OMIM: gene MIM:619676 | 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

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, increases methylation	4
Benzo(a)pyrene	increases methylation, increases expression	2
butyraldehyde	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Cisplatin	increases expression	1
Methotrexate	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Okadaic Acid	increases expression	1
Magnetite Nanoparticles	increases expression	1

Clinical trials (associated diseases)

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