SPMIP3

Summary

SPMIP3 (sperm microtubule inner protein 3, HGNC:30435) is a protein-coding gene on chromosome 1q44, encoding Protein SPMIP3 (Q5SVJ3).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_001012970

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30435
Approved symbol	SPMIP3
Name	sperm microtubule inner protein 3
Location	1q44
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000173728
Ensembl biotype	protein_coding
Entrez	200159

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000308105, ENST00000366537, ENST00000470211, ENST00000486803

RefSeq mRNA: 3 — MANE Select: NM_001012970 NM_001012970, NM_001276348, NM_001276349

CCDS: CCDS31079, CCDS60465

Canonical transcript exons

ENST00000308105 — 5 exons

Exon	Start	End
ENSE00001207943	244378467	244378639
ENSE00001333032	244352635	244352734
ENSE00003459745	244375372	244375467
ENSE00003663955	244364688	244364756
ENSE00003888946	244388951	244389663

Expression profiles

Bgee: expression breadth ubiquitous, 148 present calls, max score 93.59.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1917 / max 179.5318, expressed in 10 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9471	0.1917	10

Top tissues by expression

254 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	93.59	gold quality
left testis	UBERON:0004533	91.15	gold quality
right testis	UBERON:0004534	90.82	gold quality
testis	UBERON:0000473	88.34	gold quality
sperm	CL:0000019	82.50	gold quality
adult organism	UBERON:0007023	77.48	gold quality
buccal mucosa cell	CL:0002336	74.43	gold quality
granulocyte	CL:0000094	70.30	gold quality
adrenal tissue	UBERON:0018303	63.11	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	63.10	gold quality
monocyte	CL:0000576	60.58	gold quality
mucosa of transverse colon	UBERON:0004991	60.54	gold quality
leukocyte	CL:0000738	60.46	gold quality
tibialis anterior	UBERON:0001385	59.80	silver quality
ileal mucosa	UBERON:0000331	57.08	silver quality
lower lobe of lung	UBERON:0008949	56.87	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	56.08	gold quality
spleen	UBERON:0002106	55.26	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
lower esophagus mucosa	UBERON:0035834	53.61	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
epithelial cell of pancreas	CL:0000083	53.43	gold quality
deltoid	UBERON:0001476	53.35	gold quality
metanephros cortex	UBERON:0010533	53.19	gold quality
left uterine tube	UBERON:0001303	52.44	gold quality
right adrenal gland	UBERON:0001233	52.03	gold quality
nasal cavity mucosa	UBERON:0001826	52.02	gold quality
body of stomach	UBERON:0001161	52.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.77

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmip3	ENSMUSG00000015962
rattus_norvegicus	Spmip3	ENSRNOG00000021411

Protein

Protein identifiers

Protein SPMIP3 — Q5SVJ3 (reviewed: Q5SVJ3)

Alternative names: Sperm-associated microtubule inner protein 3

All UniProt accessions (1): Q5SVJ3

Isoforms (2)

UniProt ID	Names	Canonical?
Q5SVJ3-1	1	yes
Q5SVJ3-2	2

RefSeq proteins (3): NP_001012988, NP_001263277, NP_001263278 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037668	SPMIP3	Family

Pfam: PF17670

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SVJ3-F1	63.65	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, chr1q44, CHEN_METABOLIC_SYNDROM_NETWORK, SUPT16H_TARGET_GENES, ZIM3_TARGET_GENES, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_2H_ACT_CD4_TCELL_DN, GSE29615_DAY3_VS_DAY7_LAIV_FLU_VACCINE_PBMC_DN, GSE30962_PRIMARY_VS_SECONDARY_ACUTE_LCMV_INF_CD8_TCELL_DN, TCGA_GLIOBLASTOMA_COPY_NUMBER_UP, GSE7460_CTRL_VS_TGFB_TREATED_ACT_FOXP3_MUT_TCONV_DN, GSE19772_CTRL_VS_HCMV_INF_MONOCYTES_AND_PI3K_INHIBITION_UP, GSE26351_UNSTIM_VS_BMP_PATHWAY_STIM_HEMATOPOIETIC_PROGENITORS_UP, GSE30971_2H_VS_4H_LPS_STIM_MACROPHAGE_WBP7_HET_DN, GSE11961_PLASMA_CELL_DAY7_VS_GERMINAL_CENTER_BCELL_DAY40_UP, GSE42724_NAIVE_VS_MEMORY_BCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

174 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMIP3	ZNF672	Q499Z4	604
SPMIP3	TEX35	Q5T0J7	479
SPMIP3	DESI2	Q9BSY9	476
SPMIP3	ZBTB18	Q99592	468
SPMIP3	CATSPERE	Q5SY80	446
SPMIP3	ZNF695	Q8IW36	371
SPMIP3	CARMIL1	Q5VZK9	365
SPMIP3	DENND1B	Q6P3S1	328
SPMIP3	GORAB	Q5T7V8	325
SPMIP3	CFAP45	Q9UL16	325
SPMIP3	CHRNA5	P30532	324
SPMIP3	SLMAP	Q14BN4	321
SPMIP3	CRCT1	Q9UGL9	311
SPMIP3	CIART	Q8N365	310
SPMIP3	ANXA9	O76027	310

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A3Q1MT14, A4D263, A6NL82, A6QQL5, A8QW39, B0UXH9, B5X5D0, B9EJX3, E1B9R1, F1MMV1, Q148A4, Q1JPL0, Q2T9T0, Q32KQ1, Q32L72, Q32L77, Q32P67, Q3V0J4, Q5BN46, Q5NC57, Q5NC83, Q5SPV6, Q5SS90, Q5SVJ3, Q5VTT2, Q5VZQ5, Q66HC0, Q66HR9, Q6AYM0, Q6NXP0, Q6P3G4, Q6ZVS7, Q80X60, Q8CDT5, Q8CDU5, Q8N5S3, Q8N7U6, Q8N865

Diamond homologs: Q32L72, Q5SVJ3, Q9DAA7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

9 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

944 predictions. Top by Δscore:

Variant	Effect	Δscore
1:244375358:A:AG	acceptor_gain	0.9900
1:244375370:A:AG	acceptor_gain	0.9900
1:244375371:G:GG	acceptor_gain	0.9900
1:244375371:GT:G	acceptor_gain	0.9900
1:244375371:GTAT:G	acceptor_gain	0.9900
1:244352733:AG:A	donor_loss	0.9800
1:244352734:GGT:G	donor_loss	0.9800
1:244352735:GTAAT:G	donor_loss	0.9800
1:244352736:T:G	donor_loss	0.9800
1:244364686:A:AG	acceptor_gain	0.9800
1:244364687:G:GG	acceptor_gain	0.9800
1:244388943:A:G	acceptor_gain	0.9800
1:244388949:A:AG	acceptor_gain	0.9800
1:244388949:AGATT:A	acceptor_gain	0.9800
1:244388950:G:GG	acceptor_gain	0.9800
1:244388950:GATTG:G	acceptor_gain	0.9800
1:244352706:G:GT	donor_gain	0.9700
1:244358917:GGGA:G	acceptor_gain	0.9700
1:244358989:GATG:G	donor_gain	0.9700
1:244358991:TGG:T	donor_loss	0.9700
1:244358994:TAAGT:T	donor_loss	0.9700
1:244358995:AAGT:A	donor_loss	0.9700
1:244375359:C:G	acceptor_gain	0.9700
1:244388942:A:AG	acceptor_gain	0.9700
1:244388945:TTCCA:T	acceptor_loss	0.9700
1:244388946:TCCAG:T	acceptor_loss	0.9700
1:244388947:CCAG:C	acceptor_loss	0.9700
1:244388948:CAG:C	acceptor_loss	0.9700
1:244388949:AGA:A	acceptor_loss	0.9700
1:244388950:GATT:G	acceptor_gain	0.9700

AlphaMissense

938 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:244364725:T:C	F9L	0.965
1:244364727:T:A	F9L	0.965
1:244364727:T:G	F9L	0.965
1:244378627:T:C	F105L	0.928
1:244378629:T:A	F105L	0.928
1:244378629:T:G	F105L	0.928
1:244375391:G:A	G26R	0.894
1:244375391:G:C	G26R	0.894
1:244375406:G:C	G31R	0.892
1:244375428:C:A	A38E	0.869
1:244364726:T:C	F9S	0.868
1:244378526:A:T	D71V	0.867
1:244378538:T:C	L75P	0.861
1:244375432:A:C	R39S	0.860
1:244375432:A:T	R39S	0.860
1:244378527:C:A	D71E	0.833
1:244378527:C:G	D71E	0.833
1:244375392:G:A	G26E	0.830
1:244375407:G:A	G31D	0.829
1:244378538:T:A	L75H	0.829
1:244378598:C:T	T95I	0.816
1:244378525:G:C	D71H	0.810
1:244378526:A:C	D71A	0.807
1:244378610:G:C	R99P	0.794
1:244364726:T:G	F9C	0.793
1:244378603:T:G	Y97D	0.793
1:244375438:T:A	H41Q	0.782
1:244375438:T:G	H41Q	0.782
1:244378585:T:A	W91R	0.782
1:244378585:T:C	W91R	0.782

dbSNP variants (sampled 300 via entrez): RS1000164440 (1:244381385 T>C), RS1000215417 (1:244375774 C>T), RS1000219792 (1:244376108 G>A,C), RS1000418125 (1:244371619 A>G), RS1000448352 (1:244357664 T>A,C), RS1000623360 (1:244386893 C>T), RS1000633653 (1:244351531 A>C), RS1000669124 (1:244351861 C>T), RS1000725382 (1:244357514 G>A,T), RS1000790535 (1:244371298 G>A), RS1000811179 (1:244363243 A>G), RS1000912163 (1:244361888 T>C), RS1000933468 (1:244357759 A>C,T), RS1000985438 (1:244362151 T>C), RS1001005457 (1:244351157 G>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

3 associations (top):

Study	Trait	p-value
GCST001502_1	Asthma (childhood onset)	6.000000e-06
GCST001539_2	Smoking behavior	3.000000e-07
GCST006633_1	Initial alcohol sensitivity	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004318	smoking behavior

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
bisphenol A	affects cotreatment, affects methylation	1
Fulvestrant	affects cotreatment, affects methylation	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Diethylhexyl Phthalate	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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