SHCBP1L

gene
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Summary

SHCBP1L (SHC binding and spindle associated 1 like, HGNC:16788) is a protein-coding gene on chromosome 1q25.3, encoding Testicular spindle-associated protein SHCBP1L (Q9BZQ2). Testis-specific spindle-associated factor that plays a role in spermatogenesis.

This gene encodes a Src homology 2 domain-binding protein 1-like protein. The encoded protein interacts with heat shock 70 kDa protein 2 and may be involved in maintaining spindle integrity during meiosis. This gene is located in region of chromoso0me 1 encompassing a prostate cancer susceptibility locus.

Source: NCBI Gene 81626 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 120 total
  • MANE Select transcript: NM_030933

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16788
Approved symbolSHCBP1L
NameSHC binding and spindle associated 1 like
Location1q25.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000157060
Ensembl biotypeprotein_coding
OMIM619514
Entrez81626

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000367547, ENST00000467208, ENST00000483655, ENST00000488956, ENST00000497549

RefSeq mRNA: 2 — MANE Select: NM_030933 NM_001345928, NM_030933

CCDS: CCDS30955

Canonical transcript exons

ENST00000367547 — 10 exons

ExonStartEnd
ENSE00001900619182952729182953166
ENSE00003484713182903039182903161
ENSE00003550352182904180182904430
ENSE00003562230182939467182939553
ENSE00003605306182929647182929752
ENSE00003633223182899865182900234
ENSE00003664512182951318182951467
ENSE00003678002182940329182940543
ENSE00003687127182939176182939394
ENSE00003687583182905496182905649

Expression profiles

Bgee: expression breadth broad, 53 present calls, max score 97.27.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3880 / max 323.4279, expressed in 17 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
161720.388017

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001997.27gold quality
right testisUBERON:000453497.25gold quality
left testisUBERON:000453397.23gold quality
male germ cellCL:000001596.47gold quality
testisUBERON:000047394.04gold quality
adult organismUBERON:000702391.32gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.64gold quality
diaphragmUBERON:000110375.20gold quality
olfactory bulbUBERON:000226470.74gold quality
type B pancreatic cellCL:000016969.81gold quality
triceps brachiiUBERON:000150964.05gold quality
cervix squamous epitheliumUBERON:000692263.91gold quality
tongue squamous epitheliumUBERON:000691961.68gold quality
gluteal muscleUBERON:000200061.65gold quality
nephron tubuleUBERON:000123160.36gold quality
cervix epitheliumUBERON:000480159.93gold quality
CA1 field of hippocampusUBERON:000388159.70gold quality
orbitofrontal cortexUBERON:000416759.59gold quality
pancreatic ductal cellCL:000207959.30silver quality
mucosa of urinary bladderUBERON:000125958.36gold quality
thymusUBERON:000237057.44gold quality
quadriceps femorisUBERON:000137756.76gold quality
nasal cavity epitheliumUBERON:000538456.68gold quality
vastus lateralisUBERON:000137955.54gold quality
deltoidUBERON:000147655.54gold quality
metanephric glomerulusUBERON:000473654.81gold quality
vena cavaUBERON:000408754.55gold quality
lower lobe of lungUBERON:000894954.47silver quality
oviduct epitheliumUBERON:000480454.39gold quality
cerebellar vermisUBERON:000472054.19gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-124263yes946.10
E-GEOD-134144yes770.29
E-ANND-3no4.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting SHCBP1L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-6516-3P99.6568.571238
HSA-MIR-445299.5068.451493
HSA-MIR-302B-5P99.5069.491857
HSA-MIR-302D-5P99.5069.341863
HSA-MIR-183-3P99.4169.411598
HSA-MIR-758-3P98.4268.601122
HSA-MIR-96-3P97.4768.03839
HSA-MIR-194-3P97.3665.961027
HSA-MIR-6742-5P96.3264.01869

Literature-anchored findings (GeneRIF, showing 1)

  • SHCBP1L is a conserved mammalian protein predominantly expressed in male germ cells and it maintains spindle stability during meiosis in testis. (PMID:24557841)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusShcbp1lENSMUSG00000042708
rattus_norvegicusShcbp1lENSRNOG00000002691

Paralogs (1): SHCBP1 (ENSG00000171241)

Protein

Protein identifiers

Testicular spindle-associated protein SHCBP1LQ9BZQ2 (reviewed: Q9BZQ2)

Alternative names: SHC SH2 domain-binding protein 1-like protein

All UniProt accessions (1): Q9BZQ2

UniProt curated annotations — full annotation on UniProt →

Function. Testis-specific spindle-associated factor that plays a role in spermatogenesis. In association with HSPA2, participates in the maintenance of spindle integrity during meiosis in male germ cells.

Subunit / interactions. Interacts with HSPA2; this interaction may promote the recruitment of HSPA2 to the spindle.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle.

Tissue specificity. Expressed in spermatocytes and elongating spermatids inside the seminiferous tubules (at protein level). Testis-specific.

Isoforms (3)

UniProt IDNamesCanonical?
Q9BZQ2-33yes
Q9BZQ2-22
Q9BZQ2-44

RefSeq proteins (2): NP_001332857, NP_112195* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006626PbH1Repeat
IPR006633Carb-bd_sugar_hydrolysis-domDomain
IPR011050Pectin_lyase_fold/virulenceHomologous_superfamily
IPR012334Pectin_lyas_foldHomologous_superfamily
IPR039448Beta_helixDomain
IPR045140SHCBP1-likeFamily
IPR057508SHCBP-like_NDomain

Pfam: PF13229, PF23762

UniProt features (20 total): repeat 4, modified residue 4, splice variant 4, sequence conflict 2, compositionally biased region 2, chain 1, sequence variant 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BZQ2-F177.610.47

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 53, 570, 645, 8

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 72 (showing top): GOBP_CHROMOSOME_ORGANIZATION, MYOGENIN_Q6, GOBP_MALE_GAMETE_GENERATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, AAAYRNCTG_UNKNOWN, GOBP_ORGANELLE_FISSION, MYOD_01, GOBP_CYTOKINESIS, GRE_C, MYOD_Q6, IK2_01, GOBP_POSITIVE_REGULATION_OF_CHROMOSOME_ORGANIZATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, GOBP_REGULATION_OF_CHROMOSOME_ORGANIZATION

GO Biological Process (4): male meiosis cytokinesis (GO:0007112), spermatogenesis (GO:0007283), cell differentiation (GO:0030154), positive regulation of chromosome organization (GO:2001252)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): meiotic spindle (GO:0072687), cytoplasm (GO:0005737), spindle (GO:0005819), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle2
male meiotic nuclear division1
meiotic cytokinesis1
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1
positive regulation of organelle organization1
regulation of chromosome organization1
chromosome organization1
binding1
spindle1
intracellular anatomical structure1
cellular anatomical structure1
microtubule cytoskeleton1

Protein interactions and networks

STRING

766 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SHCBP1LCABS1Q96KC9644
SHCBP1LSPATA3Q8NHX4534
SHCBP1LHSPA2P54652496
SHCBP1LTMCO5AQ8N6Q1486
SHCBP1LPDCL2Q8N4E4476
SHCBP1LTMCO2Q7Z6W1467
SHCBP1LCCDC187A0A096LP49456
SHCBP1LFBXO47Q5MNV8456
SHCBP1LCCDC54Q8NEL0446
SHCBP1LCXorf65A6NEN9445
SHCBP1LMETTL24Q5JXM2442
SHCBP1LFAM209AQ5JX71437
SHCBP1LC20orf173Q96LM9434
SHCBP1LSMIM23A6NLE4425
SHCBP1LZC3H11DQ8NA57418
SHCBP1LRNF151Q2KHN1418

IntAct

21 interactions, top by confidence:

ABTypeScore
SHCBP1LZNF835psi-mi:“MI:0915”(physical association)0.560
CASP6SHCBP1Lpsi-mi:“MI:0915”(physical association)0.560
SHCBP1LHIP1psi-mi:“MI:0915”(physical association)0.560
LAMP2SHCBP1Lpsi-mi:“MI:0915”(physical association)0.560
SH3GLB1SHCBP1Lpsi-mi:“MI:0915”(physical association)0.560
PRPF40ASHCBP1Lpsi-mi:“MI:0915”(physical association)0.560
SHCBP1LH1-1psi-mi:“MI:0915”(physical association)0.400
BRAPSHCBP1Lpsi-mi:“MI:0915”(physical association)0.370
SHCBP1LZNF835psi-mi:“MI:0915”(physical association)0.000

BioGRID (7): SHCBP1L (Synthetic Lethality), SHCBP1L (Two-hybrid), SHCBP1L (Two-hybrid), SHCBP1L (Proximity Label-MS), SHCBP1L (Affinity Capture-MS), SHCBP1L (Cross-Linking-MS (XL-MS)), UBC (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GUJ8, A1A5R7, A2CJ06, A7E3N2, B1H224, B8QB46, D3Z8Y2, D3ZSP7, O55036, P0CG32, P54274, P70371, Q14BQ3, Q29RJ0, Q2HJ46, Q2T9U5, Q3TTP0, Q4R8X0, Q4R9F7, Q4VA55, Q5DTT8, Q5RBH9, Q5TKR9, Q5U310, Q5ZIX8, Q6DJS0, Q6ZQF7, Q71M44, Q7Z2W4, Q7Z7J5, Q80VH0, Q80VM8, Q8BMD7, Q8BZ21, Q8CCG4, Q8CDN1, Q8JZW8, Q8ND61, Q8TE76, Q8VD24

Diamond homologs: Q3TTP0, Q640F2, Q8NEM2, Q9BZQ2, Q9Z179, Q6GPE9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance110
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1967 predictions. Top by Δscore:

VariantEffectΔscore
1:182903160:CC:Cacceptor_gain1.0000
1:182903160:CCCT:Cacceptor_loss1.0000
1:182903161:CC:Cacceptor_gain1.0000
1:182903162:CTGT:Cacceptor_loss1.0000
1:182903163:T:Aacceptor_loss1.0000
1:182905494:AC:Adonor_gain1.0000
1:182905495:CC:Cdonor_gain1.0000
1:182939192:C:Adonor_gain1.0000
1:182939458:TATAC:Tdonor_loss1.0000
1:182939459:ATAC:Adonor_loss1.0000
1:182939460:TAC:Tdonor_loss1.0000
1:182939461:ACTT:Adonor_loss1.0000
1:182939462:CT:Cdonor_loss1.0000
1:182939463:T:TCdonor_loss1.0000
1:182939464:T:TGdonor_loss1.0000
1:182939465:A:ACdonor_gain1.0000
1:182939465:AC:Adonor_loss1.0000
1:182939466:C:CAdonor_gain1.0000
1:182939466:CA:Cdonor_gain1.0000
1:182939466:CAA:Cdonor_gain1.0000
1:182939466:CAAA:Cdonor_gain1.0000
1:182939466:CAAAT:Cdonor_gain1.0000
1:182939552:ACCTA:Aacceptor_loss1.0000
1:182940323:TAATA:Tdonor_loss1.0000
1:182940325:ATAC:Adonor_loss1.0000
1:182940326:TA:Tdonor_loss1.0000
1:182940327:ACCTG:Adonor_loss1.0000
1:182940330:TGACA:Tdonor_gain1.0000
1:182940338:T:TAdonor_gain1.0000
1:182940371:T:Cdonor_gain1.0000

AlphaMissense

4305 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:182939525:A:GW267R0.999
1:182939525:A:TW267R0.999
1:182939243:A:GW337R0.998
1:182939243:A:TW337R0.998
1:182939302:A:GL317P0.998
1:182939475:T:AR283S0.998
1:182939475:T:GR283S0.998
1:182939476:C:GR283T0.998
1:182939529:T:AR265S0.998
1:182939529:T:GR265S0.998
1:182939530:C:GR265T0.998
1:182903132:G:CS539R0.997
1:182903132:G:TS539R0.997
1:182903134:T:GS539R0.997
1:182939203:A:GL350P0.997
1:182939476:C:AR283I0.997
1:182939523:C:AW267C0.997
1:182939523:C:GW267C0.997
1:182951322:A:TV184D0.997
1:182951392:A:GW161R0.997
1:182951392:A:TW161R0.997
1:182903151:A:TV533D0.996
1:182904198:A:CS523R0.996
1:182904198:A:TS523R0.996
1:182904200:T:GS523R0.996
1:182904232:A:TV512D0.996
1:182939195:A:GW353R0.996
1:182939195:A:TW353R0.996
1:182939522:C:GD268H0.996
1:182951404:A:GW157R0.996

dbSNP variants (sampled 300 via entrez): RS1000249692 (1:182933978 G>A), RS1000259659 (1:182930578 T>C), RS1000310805 (1:182914950 A>C), RS1000399429 (1:182940330 T>C,G), RS1000410769 (1:182939962 A>C), RS1000530020 (1:182919880 G>A), RS1000604470 (1:182929917 A>G), RS1000757469 (1:182926672 T>C), RS1000778738 (1:182945084 C>T), RS1000782957 (1:182903087 G>A,C), RS1000831748 (1:182953768 A>G), RS1000895117 (1:182922421 G>A), RS1000906225 (1:182951683 G>A), RS1000920197 (1:182903418 A>G,T), RS1000921414 (1:182900330 T>C,G)

Disease associations

OMIM: gene MIM:619514 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): prostate cancer (MONDO:0008315)

Orphanet (1): Familial prostate cancer (Orphanet:1331)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST007565_117Morning person2.000000e-24
GCST011741_66LDL cholesterol levels in HIV infection4.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008328chronotype measurement
EFO:0004611low density lipoprotein cholesterol measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

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.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation1
Estradiolincreases expression1
Methotrexatedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.