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SPMIP7

gene
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Summary

SPMIP7 (sperm microtubule inner protein 7, HGNC:22564) is a protein-coding gene on chromosome 7p12.2, encoding Protein SPMIP7 (A4D263). Essential for normal spermatogenesis.

Predicted to be involved in spermatogenesis.

Source: NCBI Gene 100130988 — RefSeq curated summary.

At a glance

  • GWAS associations: 37
  • Clinical variants (ClinVar): 8 total
  • MANE Select transcript: NM_001161834

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:22564
Approved symbolSPMIP7
Namesperm microtubule inner protein 7
Location7p12.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000164500
Ensembl biotypeprotein_coding
Entrez100130988

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000297001

RefSeq mRNA: 1 — MANE Select: NM_001161834 NM_001161834

CCDS: CCDS47585

Canonical transcript exons

ENST00000297001 — 9 exons

ExonStartEnd
ENSE000010849055013609850136165
ENSE000012448235014014050140181
ENSE000012448355015145050151557
ENSE000013269005015904650159256
ENSE000016077165009588350096638
ENSE000016083785012971750129793
ENSE000016170455014128150141388
ENSE000018052195013410850134246
ENSE000018062675010431450104411

Expression profiles

Bgee: expression breadth broad, 19 present calls, max score 62.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0106 / max 7.6684, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
786130.01063

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453362.64gold quality
testisUBERON:000047362.47gold quality
right testisUBERON:000453461.92gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099154.83gold quality
nucleus accumbensUBERON:000188248.03gold quality
colonic epitheliumUBERON:000039741.66gold quality
caudate nucleusUBERON:000187340.19gold quality
putamenUBERON:000187439.25gold quality
duodenumUBERON:000211439.14gold quality
amygdalaUBERON:000187639.04gold quality
temporal lobeUBERON:000187138.92gold quality
lymph nodeUBERON:000002938.74gold quality
pituitary glandUBERON:000000737.03gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
bone marrow cellCL:000209236.16gold quality
adenohypophysisUBERON:000219635.63gold quality
ganglionic eminenceUBERON:000402335.49gold quality
tonsilUBERON:000237234.98gold quality
monocyteCL:000057634.91gold quality
leukocyteCL:000073834.25gold quality
prefrontal cortexUBERON:000045134.06silver quality
vermiform appendixUBERON:000115433.47silver quality
skeletal muscle tissueUBERON:000113433.38gold quality
mucosa of stomachUBERON:000119932.71gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
muscle tissueUBERON:000238532.14gold quality
brainUBERON:000095532.05gold quality
bone marrowUBERON:000237131.74gold quality
sural nerveUBERON:001548830.93gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.11

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

  • In humans and mice with azoospermia, expression of SPATA48 disappeared in the testis. (PMID:29700843)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioSPMIP7ENSDARG00000109818
mus_musculusSpmip7ENSMUSG00000020191
rattus_norvegicusSpmip7ENSRNOG00000037621

Protein

Protein identifiers

Protein SPMIP7 — A4D263 (reviewed: A4D263)

Alternative names: Sperm microtubule inner protein 7, Spermatogenesis-associated protein 48

All UniProt accessions (1): A4D263

UniProt curated annotations — full annotation on UniProt →

Function. Essential for normal spermatogenesis.

Tissue specificity. Testis-specific.

Induction. Down-regulated expression in testicular samples of azoospermic men.

RefSeq proteins (1): NP_001155306* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR027867SPATA48Family

Pfam: PF15073

UniProt features (3 total): sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A4D263-F155.760.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ZHENG_BOUND_BY_FOXP3, chr7p12, DESCARTES_MAIN_FETAL_EPICARDIAL_FAT_CELLS, GOBP_SEXUAL_REPRODUCTION, GSE26669_CD4_VS_CD8_TCELL_IN_MLR_COSTIM_BLOCK_UP, GSE27786_BCELL_VS_CD4_TCELL_UP, GOBP_REPRODUCTIVE_PROCESS, GOBP_MULTICELLULAR_ORGANISMAL_REPRODUCTIVE_PROCESS, GSE8835_CD4_VS_CD8_TCELL_DN, GSE2585_CTEC_VS_THYMIC_DC_UP, GSE5455_HEALTHY_VS_TUMOR_BEARING_MOUSE_SPLEEN_MONOCYTE_24H_INCUBATION_UP, GSE16385_MONOCYTE_VS_MACROPHAGE_DN, GSE25123_CTRL_VS_IL4_AND_ROSIGLITAZONE_STIM_MACROPHAGE_DN

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1

Protein interactions and networks

STRING

252 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SPMIP7PRR35P0CG20616
SPMIP7KBTBD12Q3ZCT8554
SPMIP7RRP36Q96EU6538
SPMIP7FIGNL1Q6PIW4520
SPMIP7KLHDC8BQ8IXV7517
SPMIP7ZPBPQ9BS86501
SPMIP7TOGARAM1Q9Y4F4501
SPMIP7TRAPPC6BQ86SZ2492
SPMIP7SIRAL2Q9NWS6476
SPMIP7KCNG3Q8TAE7475
SPMIP7SIPA1L2Q9P2F8472
SPMIP7THSD7AQ9UPZ6457
SPMIP7DNASE2O00115455
SPMIP7RAB11FIP3O75154452
SPMIP7VWC2Q2TAL6416

IntAct

4 interactions, top by confidence:

ABTypeScore
SPMIP7MAGT1psi-mi:“MI:0915”(physical association)0.400
SPMIP7ZMPSTE24psi-mi:“MI:0915”(physical association)0.400
SPMIP7RPLP2psi-mi:“MI:0915”(physical association)0.400

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: A4D263, Q5NC83

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance5
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1344 predictions. Top by Δscore:

VariantEffectΔscore
7:50104407:GTACA:Gdonor_gain1.0000
7:50104412:G:GGdonor_gain1.0000
7:50141385:GTCG:Gdonor_gain1.0000
7:50151435:A:AGacceptor_gain1.0000
7:50151448:A:AGacceptor_gain1.0000
7:50151449:G:GGacceptor_gain1.0000
7:50151558:G:GAdonor_loss1.0000
7:50151558:G:GGdonor_gain1.0000
7:50151559:TAA:Tdonor_loss1.0000
7:50104362:G:GTdonor_gain0.9900
7:50104370:T:TGdonor_gain0.9900
7:50104397:G:GTdonor_gain0.9900
7:50104430:T:TAdonor_gain0.9900
7:50104431:G:GAdonor_gain0.9900
7:50141271:A:AGacceptor_gain0.9900
7:50141272:T:Gacceptor_gain0.9900
7:50141276:A:AGacceptor_gain0.9900
7:50141279:A:AGacceptor_gain0.9900
7:50141279:AGT:Aacceptor_gain0.9900
7:50141280:G:GAacceptor_gain0.9900
7:50141280:GT:Gacceptor_gain0.9900
7:50141280:GTG:Gacceptor_gain0.9900
7:50141280:GTGGT:Gacceptor_gain0.9900
7:50151436:A:Gacceptor_gain0.9900
7:50151449:GT:Gacceptor_gain0.9900
7:50151553:CACCG:Cdonor_gain0.9900
7:50151555:CCG:Cdonor_gain0.9900
7:50151556:CG:Cdonor_gain0.9900
7:50151557:GG:Gdonor_gain0.9900
7:50151560:AA:Adonor_loss0.9900

AlphaMissense

2872 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:50096419:A:CS112R0.972
7:50096421:T:AS112R0.972
7:50096421:T:GS112R0.972
7:50134127:T:AW250R0.970
7:50134127:T:CW250R0.970
7:50159134:T:CF428L0.957
7:50159136:C:AF428L0.957
7:50159136:C:GF428L0.957
7:50140144:A:CS314R0.941
7:50140146:T:AS314R0.941
7:50140146:T:GS314R0.941
7:50096590:T:AW169R0.940
7:50096590:T:CW169R0.940
7:50134129:G:CW250C0.936
7:50134129:G:TW250C0.936
7:50136164:T:CF312L0.925
7:50140140:T:AF312L0.925
7:50140140:T:GF312L0.925
7:50096284:T:CF67L0.915
7:50096286:T:AF67L0.915
7:50096286:T:GF67L0.915
7:50159130:C:AN426K0.913
7:50159130:C:GN426K0.913
7:50136122:T:CF298L0.906
7:50136124:T:AF298L0.906
7:50136124:T:GF298L0.906
7:50096275:T:CF64L0.905
7:50096277:T:AF64L0.905
7:50096277:T:GF64L0.905
7:50096592:G:CW169C0.900

dbSNP variants (sampled 300 via entrez): RS1000000584 (7:50094801 T>C), RS1000055926 (7:50135091 T>C,G), RS1000077558 (7:50140621 A>C), RS1000078502 (7:50109072 C>A), RS1000102925 (7:50123970 A>C,T), RS1000177584 (7:50102161 TA>T), RS1000252010 (7:50107097 T>G), RS1000323018 (7:50142400 A>C), RS1000327839 (7:50095309 T>A), RS1000372754 (7:50114663 A>G), RS1000381650 (7:50095565 A>C), RS1000383541 (7:50152371 T>C), RS1000548928 (7:50118801 G>A), RS1000550963 (7:50149128 C>G,T), RS1000552895 (7:50101008 G>A)

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

37 associations (top):

StudyTraitp-value
GCST003599_8Systemic lupus erythematosus2.000000e-16
GCST003995_13Tonsillectomy1.000000e-11
GCST004131_94Inflammatory bowel disease5.000000e-11
GCST004132_57Crohn’s disease9.000000e-12
GCST004785_10Vitiligo2.000000e-07
GCST004861_92Itch intensity from mosquito bite3.000000e-12
GCST004862_6Itch intensity from mosquito bite adjusted by bite size1.000000e-07
GCST004862_80Itch intensity from mosquito bite adjusted by bite size1.000000e-07
GCST004863_95Mosquito bite size1.000000e-08
GCST005014_146Tonsillectomy1.000000e-11
GCST005038_115Allergic disease (asthma, hay fever or eczema)6.000000e-11
GCST005537_211Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)2.000000e-09
GCST005752_165Systemic lupus erythematosus3.000000e-14
GCST005752_56Systemic lupus erythematosus1.000000e-06
GCST005950_9Body mass index x sex x age interaction (4df test)2.000000e-09
GCST005951_200Body mass index2.000000e-08
GCST005951_57Body mass index3.000000e-10
GCST005953_3Body mass index (age <50)8.000000e-10
GCST005977_2Monocyte count1.000000e-10
GCST005987_44Albumin-globulin ratio5.000000e-23
GCST005989_18Serum total protein levels1.000000e-10
GCST005990_30Non-albumin protein levels1.000000e-23
GCST005999_15Aspartate aminotransferase levels3.000000e-08
GCST006005_12High density lipoprotein cholesterol levels5.000000e-10
GCST006034_22Total cholesterol levels8.000000e-09
GCST006097_4Moderate to vigorous physical activity levels6.000000e-10
GCST009066_11Mosaic loss of chromosome Y (Y chromosome dosage)4.000000e-19
GCST009067_13Mosaic loss of chromosome Y (Y chromosome dosage)4.000000e-21
GCST009597_10Multiple sclerosis3.000000e-16
GCST009597_4Multiple sclerosis8.000000e-11

EFO canonical traits (16, from GWAS)

EFO IDTrait name
EFO:0007924tonsillectomy risk measurement
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0004340body mass index
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0005091monocyte count
EFO:0005128albumin:globulin ratio measurement
EFO:0004736aspartate aminotransferase measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004574total cholesterol measurement
EFO:0008002physical activity measurement
EFO:0007783mosaic loss of chromosome Y measurement
EFO:0004614apolipoprotein A 1 measurement
EFO:0004847age at onset
EFO:0004842eosinophil count

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.

ChemicalActions (top 5)PubMed papers
Arsenicaffects methylation1
Valproic Aciddecreases methylation1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot