SPMIP2

Summary

SPMIP2 (sperm microtubule inner protein 2, HGNC:26342) is a protein-coding gene on chromosome 4q32.1, encoding Protein SPMIP2 (Q96LM5).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_152543

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26342
Approved symbol	SPMIP2
Name	sperm microtubule inner protein 2
Location	4q32.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25371
Ensembl gene	ENSG00000164123
Ensembl biotype	protein_coding
Entrez	152940

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000434826, ENST00000505647, ENST00000508011

RefSeq mRNA: 1 — MANE Select: NM_152543 NM_152543

CCDS: CCDS47156

Canonical transcript exons

ENST00000434826 — 5 exons

Exon	Start	End
ENSE00001081683	158960286	158960344
ENSE00001170830	159035033	159035229
ENSE00002083800	158893134	158893717
ENSE00003529484	158973079	158973311
ENSE00003553302	158915170	158915359

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 94.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0309 / max 17.2365, expressed in 8 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
54640	0.0174	5
54637	0.0066	3
54638	0.0041	3
54639	0.0027	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.81	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.37	gold quality
left testis	UBERON:0004533	80.97	gold quality
right testis	UBERON:0004534	80.36	gold quality
secondary oocyte	CL:0000655	79.57	silver quality
testis	UBERON:0000473	78.77	gold quality
oocyte	CL:0000023	67.73	gold quality
ventricular zone	UBERON:0003053	62.45	gold quality
adult organism	UBERON:0007023	60.29	silver quality
tibial nerve	UBERON:0001323	57.51	gold quality
monocyte	CL:0000576	53.50	gold quality
leukocyte	CL:0000738	52.46	gold quality
hindlimb stylopod muscle	UBERON:0004252	49.26	gold quality
prefrontal cortex	UBERON:0000451	48.75	gold quality
adrenal tissue	UBERON:0018303	48.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	47.95	silver quality
Brodmann (1909) area 9	UBERON:0013540	47.77	gold quality
sural nerve	UBERON:0015488	47.77	gold quality
calcaneal tendon	UBERON:0003701	46.45	silver quality
frontal cortex	UBERON:0001870	46.38	gold quality
bone marrow	UBERON:0002371	46.35	gold quality
ganglionic eminence	UBERON:0004023	46.32	gold quality
right frontal lobe	UBERON:0002810	46.31	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	45.86	gold quality
neocortex	UBERON:0001950	45.62	gold quality
smooth muscle tissue	UBERON:0001135	44.36	gold quality
cerebral cortex	UBERON:0000956	44.31	gold quality
anterior cingulate cortex	UBERON:0009835	43.45	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
lower lobe of lung	UBERON:0008949	43.00	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting SPMIP2, 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-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-34B-5P	99.78	67.56	1175
HSA-MIR-449C-5P	99.78	67.63	1168
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-4752	98.71	68.04	833
HSA-MIR-8056	97.15	64.49	769

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmip2	ENSMUSG00000091685
rattus_norvegicus	Spmip2	ENSRNOG00000032009

Protein

Protein identifiers

Protein SPMIP2 — Q96LM5 (reviewed: Q96LM5)

Alternative names: Sperm-associated microtubule inner protein 2

All UniProt accessions (1): Q96LM5

RefSeq proteins (1): NP_689756* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027814	DUF4562	Family

Pfam: PF15123

UniProt features (9 total): sequence variant 5, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LM5-F1	62.74	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, chr4q32, DACH1_TARGET_GENES, MIR4752, MIR4696, MIR8056, DESCARTES_MAIN_FETAL_PDE1C_ACSM3_POSITIVE_CELLS, NOTCH3_TARGET_GENES, GSE26488_CTRL_VS_PEPTIDE_INJECTION_OT2_THYMOCYTE_UP, GSE37605_C57BL6_VS_NOD_FOXP3_FUSION_GFP_TREG_UP, GSE37301_CD4_TCELL_VS_RAG2_KO_NK_CELL_UP

GO Biological Process (0):

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
binding	1

Protein interactions and networks

STRING

140 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMIP2	PGM2L1	Q6PCE3	570
SPMIP2	FNIP2	Q9P278	509
SPMIP2	TIPE1	Q8WVP5	500
SPMIP2	VEPH1	Q14D04	490
SPMIP2	GPRIN1	Q7Z2K8	482
SPMIP2	NWD2	Q9ULI1	434
SPMIP2	CACNG8	Q8WXS5	416
SPMIP2	POTED	Q86YR6	369
SPMIP2	PRSS2	P07478	369
SPMIP2	ANKRD55	Q3KP44	348
SPMIP2	ANXA8L1	Q5VT79	336
SPMIP2	GLRB	P48167	323
SPMIP2	MINDY3	Q9H8M7	323
SPMIP2	ZNF263	O14978	300
SPMIP2	DOK7	Q18PE1	292

IntAct

65 interactions, top by confidence:

A	B	Type	Score
CYSRT1	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SPMIP2	THAP1	psi-mi:“MI:0915”(physical association)	0.560
CCDC125	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
BOLL	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SPMIP2	CARD10	psi-mi:“MI:0915”(physical association)	0.560
TRAF1	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
TRIM69	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SREK1IP1	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
PRPF40A	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SPMIP2	PFDN5	psi-mi:“MI:0915”(physical association)	0.560
ZBTB24	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
BANP	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SPMIP2	MMTAG2	psi-mi:“MI:0915”(physical association)	0.560
KLHL41	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
BCL6	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SPMIP2	MAPRE3	psi-mi:“MI:0915”(physical association)	0.560
NFKBID	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
KRT40	SPMIP2	psi-mi:“MI:0915”(physical association)	0.560
SPMIP2	MDFI	psi-mi:“MI:0915”(physical association)	0.560
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
SPMIP2	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000
SPMIP2	THAP1	psi-mi:“MI:0915”(physical association)	0.000
SPMIP2	CCDC125	psi-mi:“MI:0915”(physical association)	0.000
SPMIP2	KRT40	psi-mi:“MI:0915”(physical association)	0.000
SPMIP2	MDFI	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), C4orf45 (Two-hybrid), NFKBID (Two-hybrid), POLR1C (Two-hybrid), BANP (Two-hybrid), CCDC57 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVB3, A0A1B0GVH6, A2RRY8, A4IGV6, A6NHR8, B3DHS1, E1B9I5, O74317, O95561, P03319, P03320, P0C9Z5, P0C9Z6, P10260, P36353, P40744, P40745, Q06616, Q09280, Q09424, Q2KIL1, Q2KIR0, Q32KT7, Q32LB6, Q3T028, Q3TTI8, Q496A3, Q5NC83, Q5SQS8, Q5XIU7, Q68FQ8, Q6DFB0, Q6ZNM6, Q6ZV65, Q811V6, Q8IWA6, Q8N9R6, Q8R0E5, Q8TAL5, Q8WTQ4

Diamond homologs: Q2KIR0, Q96LM5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1857 predictions. Top by Δscore:

Variant	Effect	Δscore
4:158960345:C:CC	acceptor_gain	1.0000
4:159035028:TTTAC:T	donor_loss	1.0000
4:159035029:TTACC:T	donor_loss	1.0000
4:159035030:TACCT:T	donor_loss	1.0000
4:159035031:ACCTG:A	donor_loss	1.0000
4:159035032:C:G	donor_loss	1.0000
4:158932783:T:TA	donor_gain	0.9900
4:158954607:C:CT	donor_gain	0.9900
4:158954608:T:TT	donor_gain	0.9900
4:158895748:A:AG	acceptor_gain	0.9800
4:158895749:G:GG	acceptor_gain	0.9800
4:158932746:CAGGG:C	donor_gain	0.9800
4:159035031:A:AC	donor_gain	0.9800
4:159035032:C:CC	donor_gain	0.9800
4:158895863:GGG:G	donor_gain	0.9700
4:158895864:GGG:G	donor_gain	0.9700
4:158904608:GAA:G	donor_gain	0.9700
4:158919325:CGTG:C	donor_gain	0.9700
4:158960341:CATA:C	acceptor_gain	0.9700
4:158960343:TA:T	acceptor_gain	0.9700
4:158973073:CAATA:C	donor_loss	0.9700
4:158973074:AATAC:A	donor_loss	0.9700
4:158973075:ATAC:A	donor_loss	0.9700
4:158973076:TA:T	donor_loss	0.9700
4:158973077:A:AG	donor_loss	0.9700
4:158973078:C:T	donor_loss	0.9700
4:158973079:C:A	donor_loss	0.9700
4:159007618:T:TA	donor_gain	0.9700
4:158894748:A:AG	donor_gain	0.9600
4:158895855:GT:G	donor_gain	0.9600

AlphaMissense

1217 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:158973088:A:C	F96L	0.808
4:158973088:A:T	F96L	0.808
4:158973090:A:G	F96L	0.808
4:159035037:A:C	F20L	0.804
4:159035037:A:T	F20L	0.804
4:159035039:A:G	F20L	0.804
4:158973141:A:G	W79R	0.803
4:158973141:A:T	W79R	0.803
4:158915284:G:C	F144L	0.783
4:158915284:G:T	F144L	0.783
4:158915286:A:G	F144L	0.783
4:158973166:T:A	K70N	0.771
4:158973166:T:G	K70N	0.771
4:158960287:A:G	W119R	0.770
4:158960287:A:T	W119R	0.770
4:158973139:C:A	W79C	0.768
4:158973139:C:G	W79C	0.768
4:158960294:T:A	Q116H	0.759
4:158960294:T:G	Q116H	0.759
4:158915301:A:G	W139R	0.745
4:158915301:A:T	W139R	0.745
4:158973118:A:C	F86L	0.729
4:158973118:A:T	F86L	0.729
4:158973120:A:G	F86L	0.729
4:158915299:C:A	W139C	0.716
4:158915299:C:G	W139C	0.716
4:158915316:G:T	R134S	0.713
4:158915359:C:A	W119C	0.710
4:158915359:C:G	W119C	0.710
4:159035033:C:G	G22R	0.695

dbSNP variants (sampled 300 via entrez): RS1000041316 (4:159030748 C>T), RS1000058781 (4:158906574 CTTAAT>C), RS1000062822 (4:159067939 T>A,C), RS1000066555 (4:159069943 T>C), RS1000067171 (4:159023236 C>T), RS1000079859 (4:159043229 G>A), RS1000091576 (4:159068323 T>C), RS1000106074 (4:159040093 A>G), RS1000113666 (4:158935275 T>C), RS1000150624 (4:158954552 C>T), RS1000197319 (4:158911342 C>A,T), RS1000206817 (4:159006057 C>A,T), RS1000212378 (4:158914941 C>T), RS1000248836 (4:158953742 G>A), RS1000260193 (4:158918440 A>C,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

4 associations (top):

Study	Trait	p-value
GCST005141_51	Cognitive ability (MTAG)	3.000000e-08
GCST009391_483	Metabolite levels	7.000000e-06
GCST011382_9	Systemic mastocytosis	6.000000e-08
GCST012006_10	Intralaminar thalamic nuclei volume	2.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0010389	phosphatidylcholine 40:6 measurement
EFO:0006935	thalamus volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation	1
Daunorubicin	affects response to substance	1

Clinical trials (associated diseases)

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