SPMIP1

Summary

SPMIP1 (sperm microtubule inner protein 1, HGNC:52392) is a protein-coding gene on chromosome 7q32.1, encoding Protein SPMIP1 (A0A1B0GUX0).

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001195150

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:52392
Approved symbol	SPMIP1
Name	sperm microtubule inner protein 1
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000272899
Ensembl biotype	protein_coding
Entrez	100130705

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000609480

RefSeq mRNA: 1 — MANE Select: NM_001195150 NM_001195150

CCDS: CCDS83222

Canonical transcript exons

ENST00000609480 — 2 exons

Exon	Start	End
ENSE00001890050	128866330	128866830
ENSE00003703672	128868666	128872047

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 86.51.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0653 / max 65.4073, expressed in 5 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80990	0.0421	4
80989	0.0232	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	86.51	gold quality
tibialis anterior	UBERON:0001385	85.67	silver quality
cerebellar hemisphere	UBERON:0002245	85.29	gold quality
cerebellar cortex	UBERON:0002129	85.08	gold quality
cerebellum	UBERON:0002037	82.66	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.39	gold quality
metanephros cortex	UBERON:0010533	80.53	gold quality
gastrocnemius	UBERON:0001388	77.50	gold quality
endothelial cell	CL:0000115	75.17	gold quality
muscle of leg	UBERON:0001383	74.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.72	gold quality
cortical plate	UBERON:0005343	72.72	gold quality
right frontal lobe	UBERON:0002810	72.71	gold quality
anterior cingulate cortex	UBERON:0009835	72.23	gold quality
prefrontal cortex	UBERON:0000451	71.99	gold quality
amygdala	UBERON:0001876	71.30	gold quality
neocortex	UBERON:0001950	70.88	gold quality
frontal cortex	UBERON:0001870	70.74	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	70.69	gold quality
Brodmann (1909) area 9	UBERON:0013540	69.81	gold quality
cerebral cortex	UBERON:0000956	69.51	gold quality
temporal lobe	UBERON:0001871	68.78	gold quality
metanephros	UBERON:0000081	67.95	gold quality
primary visual cortex	UBERON:0002436	67.53	gold quality
cortex of kidney	UBERON:0001225	67.49	gold quality
postcentral gyrus	UBERON:0002581	67.35	gold quality
deltoid	UBERON:0001476	66.73	silver quality
superior frontal gyrus	UBERON:0002661	66.70	gold quality
entorhinal cortex	UBERON:0002728	66.57	gold quality
brain	UBERON:0000955	66.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting SPMIP1, 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-5692A	100.00	74.40	6850
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6779-5P	99.70	65.76	2363

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spmip1	ENSMUSG00000090685
rattus_norvegicus	Spmip1	ENSRNOG00000086561

Protein

Protein identifiers

Protein SPMIP1 — A0A1B0GUX0 (reviewed: A0A1B0GUX0)

Alternative names: ATP6V1F neighbor gene protein, Protein ATP6V1FNB, Sperm-associated microtubule inner protein 1

All UniProt accessions (1): A0A1B0GUX0

RefSeq proteins (1): NP_001182079* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR054323	SPMIP1_C	Domain

Pfam: PF22589

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-A0A1B0GUX0-F1	79.65	0.36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): chr7q32, DODD_NASOPHARYNGEAL_CARCINOMA_UP, LMTK3_TARGET_GENES, ZFHX3_TARGET_GENES, MIR8068, MIR4427, MIR5589_3P, MIR556_3P, BLANCO_MELO_MERS_COV_INFECTION_MCR5_CELLS_UP, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_UP, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_A594_ACE2_EXPRESSING_CELLS_RUXOLITINIB_UP, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_INFECTION_UP, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_1H_DN, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_2H_DN, GSE26928_NAIVE_VS_CXCR5_POS_CD4_TCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

96 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPMIP1	CCDC127	Q96BQ5	640
SPMIP1	CST11	Q9H112	624
SPMIP1	CFAP61	Q8NHU2	623
SPMIP1	DEFB130A	P0DP74	598
SPMIP1	GCAT	O75600	593
SPMIP1	HOGA1	Q86XE5	590
SPMIP1	C6orf58	Q6P5S2	559
SPMIP1	FSIP2	Q5CZC0	502
SPMIP1	DNAH8	Q96JB1	474
SPMIP1	AKAP4	Q5JQC9	389
SPMIP1	TEKT5	Q96M29	387
SPMIP1	ODF4	Q2M2E3	348
SPMIP1	CIMAP1A	Q96PU9	326
SPMIP1	UBB	P02248	300
SPMIP1	IZUMO1	Q8IYV9	299

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: A0A1B0GUX0, B9EJX3

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	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1118 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:128866821:T:A	W138R	0.971
7:128866821:T:C	W138R	0.971
7:128866494:T:A	W29R	0.970
7:128866494:T:C	W29R	0.970
7:128866734:G:A	G109R	0.962
7:128866734:G:C	G109R	0.962
7:128866823:G:C	W138C	0.959
7:128866823:G:T	W138C	0.959
7:128866759:G:C	R117P	0.958
7:128866819:G:A	G137D	0.951
7:128868719:T:C	F159L	0.951
7:128868721:C:A	F159L	0.951
7:128868721:C:G	F159L	0.951
7:128866734:G:T	G109W	0.946
7:128866746:T:G	Y113D	0.946
7:128866735:G:A	G109E	0.936
7:128866785:T:G	Y126D	0.935
7:128866806:A:C	S133R	0.934
7:128866808:C:A	S133R	0.934
7:128866808:C:G	S133R	0.934
7:128866750:T:C	L114P	0.933
7:128866735:G:T	G109V	0.932
7:128866738:G:C	R110P	0.930
7:128866783:G:C	R125P	0.929
7:128866747:A:C	Y113S	0.920
7:128866822:G:C	W138S	0.920
7:128866713:G:C	G102R	0.914
7:128866746:T:C	Y113H	0.905
7:128866496:G:C	W29C	0.904
7:128866496:G:T	W29C	0.904

dbSNP variants (sampled 300 via entrez): RS1000158557 (7:128867359 A>C), RS1000367261 (7:128870159 T>C,G), RS1001111000 (7:128869076 T>C), RS1001162110 (7:128866041 G>T), RS1001422788 (7:128871129 G>A,C), RS1002337649 (7:128870680 C>A,G), RS1003559243 (7:128866903 G>C), RS1003751117 (7:128871869 AATTT>A), RS1003846461 (7:128868229 G>A,C), RS1004328690 (7:128872341 T>A), RS1004611932 (7:128871046 G>A), RS1004622091 (7:128866677 C>G,T), RS1004664486 (7:128870771 G>A), RS1004853761 (7:128869432 C>A), RS1005491506 (7:128869205 A>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
ferrous chloride	decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Cadmium	increases expression	1
Smoke	decreases expression	1
Aflatoxin B1	decreases methylation	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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