SPMIP11

Summary

SPMIP11 (sperm microtubule inner protein 11, HGNC:48628) is a protein-coding gene on chromosome 12q13.12, encoding Sperm microtubule inner protein 11 (A0A1B0GTD5). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagellum axoneme.

Predicted to be involved in flagellated sperm motility. Predicted to be located in cytoplasm; cytoskeleton; and sperm flagellum. Predicted to be active in axonemal A tubule inner sheath.

Source: NCBI Gene 255411 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001351123

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48628
Approved symbol	SPMIP11
Name	sperm microtubule inner protein 11
Location	12q13.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000257987
Ensembl biotype	protein_coding
Entrez	255411

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000548054, ENST00000548380

RefSeq mRNA: 2 — MANE Select: NM_001351123 NM_001351123, NM_001351125

CCDS: CCDS86296

Canonical transcript exons

ENST00000548380 — 4 exons

Exon	Start	End
ENSE00002369640	48765607	48765790
ENSE00002402178	48727435	48727559
ENSE00003794394	48759209	48759331
ENSE00003796439	48764851	48764995

Expression profiles

Bgee: expression breadth broad, 64 present calls, max score 87.22.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0168 / max 16.2391, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125268	0.0110	3
125269	0.0057	3

Top tissues by expression

188 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	87.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.92	gold quality
left testis	UBERON:0004533	84.12	gold quality
right testis	UBERON:0004534	83.23	gold quality
testis	UBERON:0000473	80.99	gold quality
sperm	CL:0000019	78.77	gold quality
sural nerve	UBERON:0015488	59.02	gold quality
adult organism	UBERON:0007023	57.86	gold quality
body of stomach	UBERON:0001161	53.43	gold quality
apex of heart	UBERON:0002098	53.07	gold quality
stomach	UBERON:0000945	51.29	gold quality
fundus of stomach	UBERON:0001160	47.78	gold quality
mucosa of transverse colon	UBERON:0004991	46.16	gold quality
granulocyte	CL:0000094	44.88	silver quality
rectum	UBERON:0001052	43.63	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
stromal cell of endometrium	CL:0002255	41.85	silver quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
biceps brachii	UBERON:0001507	41.18	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
duodenum	UBERON:0002114	40.90	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.79

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmip11	ENSMUSG00000022993
rattus_norvegicus	Spmip11	ENSRNOG00000057264

Protein

Protein identifiers

Sperm microtubule inner protein 11 — A0A1B0GTD5 (reviewed: A0A1B0GTD5)

Alternative names: Testis-expressed protein 49

All UniProt accessions (2): A0A1B0GTD5, A0A1B0GWC3

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagellum axoneme. May serve to reinforce and thus stabilize the microtubule structure in the sperm flagella.

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

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme.

RefSeq proteins (2): NP_001338052, NP_001338054 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038775	SPMIP11	Family

Pfam: PF22593

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTD5-F1	75.14	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, GOCC_AXONEMAL_MICROTUBULE, GOCC_9PLUS2_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, GOBP_MICROTUBULE_BASED_MOVEMENT, GOBP_CELL_MOTILITY, GSE26928_CENTR_MEMORY_VS_CXCR5_POS_CD4_TCELL_UP, GOBP_MICROTUBULE_BASED_PROCESS

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

GO Molecular Function (0):

GO Cellular Component (7): sperm flagellum (GO:0036126), axonemal A tubule inner sheath (GO:0160111), cytoplasm (GO:0005737), 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
9+2 motile cilium	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular anatomical structure	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

20 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMIP11	TNFSF12	O43508	0
SPMIP11	CLEC12A	Q5QGZ9	0
SPMIP11	CRYBG3	Q68DQ2	0
SPMIP11	SPMAP2L	P0DJG4	0
SPMIP11	MROH2A	A6NES4	0
SPMIP11	RAB44	Q7Z6P3	0
SPMIP11	SPMIP1	A0A1B0GUX0	0
SPMIP11	C11orf97	A0A1B0GVM6	0
SPMIP11	MDFIC2	A0A1B0GVS7	0
SPMIP11	CCDC180	Q9P1Z9	0

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: A0A1B0GTD5, A0A3Q1MT14, Q8CDT5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

885 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:48764982:A:C	S112R	0.972
12:48764984:C:A	S112R	0.972
12:48764984:C:G	S112R	0.972
12:48764898:A:C	S84R	0.969
12:48764900:C:A	S84R	0.969
12:48764900:C:G	S84R	0.969
12:48764949:T:A	W101R	0.933
12:48764949:T:C	W101R	0.933
12:48764865:T:C	F73L	0.927
12:48764867:C:A	F73L	0.927
12:48764867:C:G	F73L	0.927
12:48764901:T:C	F85L	0.927
12:48764903:C:A	F85L	0.927
12:48764903:C:G	F85L	0.927
12:48759304:G:C	A59P	0.890
12:48765608:T:C	F117L	0.882
12:48765610:T:A	F117L	0.882
12:48765610:T:G	F117L	0.882
12:48764895:T:C	F83L	0.871
12:48764897:C:A	F83L	0.871
12:48764897:C:G	F83L	0.871
12:48759295:T:G	Y56D	0.858
12:48727508:G:A	G10R	0.838
12:48727508:G:C	G10R	0.838
12:48764951:G:C	W101C	0.838
12:48764951:G:T	W101C	0.838
12:48764881:C:T	T78I	0.831
12:48727487:T:C	F3L	0.830
12:48727489:C:A	F3L	0.830
12:48727489:C:G	F3L	0.830

dbSNP variants (sampled 300 via entrez): RS1000080486 (12:48733616 A>G), RS1000156367 (12:48745237 C>G,T), RS1000175226 (12:48746673 C>A,T), RS1000354407 (12:48753157 A>G), RS1000393394 (12:48758810 T>C), RS1000534389 (12:48758659 C>A,G,T), RS1000575182 (12:48727554 A>G), RS1000691447 (12:48727314 A>G), RS1000807716 (12:48734212 C>A), RS1000937427 (12:48771860 A>G), RS1001051552 (12:48747195 T>C), RS1001055779 (12:48735465 A>G), RS1001087052 (12:48735253 C>G,T), RS1001240139 (12:48733840 C>T), RS1001311623 (12:48744992 C>A,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
GCST008163_48	Height	5.000000e-06
GCST009193_11	Pars opercularis volume	6.000000e-06
GCST90002407_283	White blood cell count	6.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aflatoxin B2	increases methylation	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1

Clinical trials (associated diseases)

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