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Atlas / Gene / C19orf53

C19orf53

gene
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Also known as L10KHero11LYDG10HSPC023

Summary

C19orf53 (chromosome 19 open reading frame 53, HGNC:24991) is a protein-coding gene on chromosome 19p13.13, encoding Leydig cell tumor 10 kDa protein homolog (Q9UNZ5). May have a potential role in hypercalcemia of malignancy. It is a selective cancer dependency (DepMap: 73.7% of cell lines).

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 12 total
  • Cancer dependency (DepMap): dependent in 73.7% of screened cell lines
  • MANE Select transcript: NM_014047

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24991
Approved symbolC19orf53
Namechromosome 19 open reading frame 53
Location19p13.13
Locus typegene with protein product
StatusApproved
AliasesL10K, Hero11, LYDG10, HSPC023
Ensembl geneENSG00000104979
Ensembl biotypeprotein_coding
OMIM620685
Entrez28974

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 nonsense_mediated_decay

ENST00000221576, ENST00000588234, ENST00000588841, ENST00000588858, ENST00000592760, ENST00000593274, ENST00000929642, ENST00000929643, ENST00000929644, ENST00000929645

RefSeq mRNA: 1 — MANE Select: NM_014047 NM_014047

CCDS: CCDS12298

Canonical transcript exons

ENST00000588234 — 3 exons

ExonStartEnd
ENSE000006850771377465213774707
ENSE000028161201377445613774574
ENSE000036325361377805213778773

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 155.9991 / max 1107.9898, expressed in 1828 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
174158153.34311828
1741601.7574918
1741590.8987532

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
hindlimb stylopod muscleUBERON:000425298.53gold quality
stromal cell of endometriumCL:000225598.34gold quality
apex of heartUBERON:000209898.11gold quality
adenohypophysisUBERON:000219698.10gold quality
anterior cingulate cortexUBERON:000983597.99gold quality
cingulate cortexUBERON:000302797.97gold quality
pituitary glandUBERON:000000797.87gold quality
amygdalaUBERON:000187697.86gold quality
nucleus accumbensUBERON:000188297.84gold quality
right adrenal glandUBERON:000123397.78gold quality
caudate nucleusUBERON:000187397.77gold quality
right atrium auricular regionUBERON:000663197.76gold quality
left adrenal gland cortexUBERON:003582597.75gold quality
heart left ventricleUBERON:000208497.74gold quality
left adrenal glandUBERON:000123497.70gold quality
cardiac ventricleUBERON:000208297.69gold quality
endocervixUBERON:000045897.66gold quality
left coronary arteryUBERON:000162697.63gold quality
left ovaryUBERON:000211997.62gold quality
right adrenal gland cortexUBERON:003582797.62gold quality
C1 segment of cervical spinal cordUBERON:000646997.61gold quality
right coronary arteryUBERON:000162597.57gold quality
granulocyteCL:000009497.53gold quality
right frontal lobeUBERON:000281097.53gold quality
coronary arteryUBERON:000162197.52gold quality
gastrocnemiusUBERON:000138897.51gold quality
left uterine tubeUBERON:000130397.49gold quality
adrenal cortexUBERON:000123597.46gold quality
ascending aortaUBERON:000149697.46gold quality
thoracic aortaUBERON:000151597.46gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-5yes31.18
E-CURD-85no299.99
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting C19orf53, 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-453199.9969.703181
HSA-MIR-6744-5P99.9366.82748
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-4694-3P99.7969.532640
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-465199.0667.572002
HSA-MIR-184398.9766.07838
HSA-MIR-4802-5P98.9766.26833
HSA-MIR-60898.9367.832013
HSA-MIR-5187-5P98.5467.94952
HSA-MIR-6728-5P97.7966.33891
HSA-MIR-4640-5P97.4266.331543
HSA-MIR-4670-3P97.3768.351378
HSA-MIR-4726-5P97.2465.671299
HSA-MIR-1288-3P96.8666.95536
HSA-MIR-448496.3564.08382
HSA-MIR-365796.3366.29608
HSA-MIR-391896.1364.651300
HSA-MIR-452295.7666.23742
HSA-MIR-4664-3P88.5763.7980

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 73.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43. (PMID:39117455)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriozgc:136864ENSDARG00000059816
mus_musculusD8Ertd738eENSMUSG00000019362
caenorhabditis_elegansWBGENE00010639

Protein

Protein identifiers

Leydig cell tumor 10 kDa protein homolog — Q9UNZ5 (reviewed: Q9UNZ5)

All UniProt accessions (5): A0A0A0MQS3, Q9UNZ5, K7EIU1, K7EN09, K7ESE5

UniProt curated annotations — full annotation on UniProt →

Function. May have a potential role in hypercalcemia of malignancy.

Similarity. Belongs to the UPF0390 family.

RefSeq proteins (1): NP_054766* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019034UPF0390Family

Pfam: PF09495

UniProt features (3 total): chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
8FLBELECTRON MICROSCOPY2.55
8FLAELECTRON MICROSCOPY2.63
8FLCELECTRON MICROSCOPY2.76
8IDTELECTRON MICROSCOPY2.8
8IDYELECTRON MICROSCOPY3
8INFELECTRON MICROSCOPY3
8INEELECTRON MICROSCOPY3.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UNZ5-F174.250.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): MODULE_151, CGGAARNGGCNG_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, LEE_CALORIE_RESTRICTION_NEOCORTEX_DN, MODULE_114, chr19p13, ABE_INNER_EAR, CEBPZ_TARGET_GENES, DLX4_TARGET_GENES, E2F2_TARGET_GENES, E2F5_TARGET_GENES, FOXR2_TARGET_GENES, GLI4_TARGET_GENES, NFE2L1_TARGET_GENES, NKX2_2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

980 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
C19orf53C19orf67A6NJJ6584
C19orf53CCDC124Q96CT7481
C19orf53RBM14Q96PK6453
C19orf53BBLNQ9BUW7432
C19orf53PSG11Q9UQ72420
C19orf53ZC3H15Q8WU90420
C19orf53ZNF221Q9UK13407
C19orf53YJU2BP13994406
C19orf53ZNF202O95125401
C19orf53BRME1Q0VDD7400
C19orf53GALNT10Q86SR1395
C19orf53DNAJC14Q6Y2X3376
C19orf53PSG9Q00887370
C19orf53ZSWIM4Q9H7M6353
C19orf53PALM3A6NDB9351

IntAct

49 interactions, top by confidence:

ABTypeScore
C19orf53IPO5psi-mi:“MI:0915”(physical association)0.400
HNRNPUpsi-mi:“MI:0914”(association)0.350
KDM1AKIF2Apsi-mi:“MI:0914”(association)0.350
MAPTMEX3Apsi-mi:“MI:0914”(association)0.350
MAPTC11orf98psi-mi:“MI:0914”(association)0.350
MAPTPOTEFpsi-mi:“MI:0914”(association)0.350
APPESYT2psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
MRPL34IPO5psi-mi:“MI:0914”(association)0.350
GRB7RIOK3psi-mi:“MI:0914”(association)0.350
GRB10POLRMTpsi-mi:“MI:0914”(association)0.350
MTMR11psi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
DDX3Xpsi-mi:“MI:0914”(association)0.350
PES1psi-mi:“MI:0914”(association)0.350
HNRNPDLpsi-mi:“MI:0914”(association)0.350
GTPBP10psi-mi:“MI:0914”(association)0.350
EIF3Fpsi-mi:“MI:0914”(association)0.350
POLR3Apsi-mi:“MI:0914”(association)0.350
POLRMTpsi-mi:“MI:0914”(association)0.350

BioGRID (35): C19orf53 (Co-fractionation), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-RNA), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Affinity Capture-MS), C19orf53 (Proximity Label-MS), C19orf53 (Proximity Label-MS), C19orf53 (Affinity Capture-MS)

ESM2 similar proteins: A5JSS4, B1MTI8, O88892, P02641, P06398, P09739, P0C0A9, P12620, P45378, P84101, P84102, Q05310, Q0UVD1, Q148I0, Q1E554, Q28HN4, Q28IN9, Q2KIT1, Q2TBR9, Q2TBV6, Q32P76, Q3E7B7, Q4I5Z5, Q5R5J3, Q5R6N0, Q5R7C4, Q5R8X8, Q5REM2, Q5ZHK9, Q68EY7, Q6DD17, Q6GNG8, Q6NVR5, Q6PHE8, Q75NG9, Q7SDA6, Q7ZY35, Q8MKI3, Q8NHG7, Q8R1F0

Diamond homologs: Q05310, Q148I0, Q24JV4, Q5REM2, Q8R1F0, Q9UNZ5, Q4WK56

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

304 predictions. Top by Δscore:

VariantEffectΔscore
19:13774705:A:Tdonor_gain1.0000
19:13778050:A:AGacceptor_gain1.0000
19:13778051:G:GTacceptor_gain1.0000
19:13778051:GA:Gacceptor_gain1.0000
19:13778051:GAA:Gacceptor_gain1.0000
19:13778051:GAAC:Gacceptor_gain1.0000
19:13774571:GGCG:Gdonor_gain0.9900
19:13774572:GCG:Gdonor_gain0.9900
19:13774572:GCGG:Gdonor_gain0.9900
19:13774574:GGTA:Gdonor_loss0.9900
19:13774575:G:GGdonor_gain0.9900
19:13774575:GTA:Gdonor_loss0.9900
19:13774576:T:Gdonor_loss0.9900
19:13774704:GAAG:Gdonor_gain0.9900
19:13774706:AG:Adonor_loss0.9900
19:13774707:GGTG:Gdonor_loss0.9900
19:13774708:GTGT:Gdonor_loss0.9900
19:13774743:C:Tdonor_gain0.9900
19:13778051:GAACC:Gacceptor_gain0.9900
19:13774704:G:GTdonor_gain0.9800
19:13774758:G:GAdonor_gain0.9800
19:13778046:CCTCA:Cacceptor_gain0.9800
19:13778047:CTCAG:Cacceptor_gain0.9800
19:13778048:TCA:Tacceptor_gain0.9800
19:13778049:CAGA:Cacceptor_gain0.9800
19:13778050:A:ATacceptor_gain0.9800
19:13778051:G:Aacceptor_gain0.9800
19:13774570:AGGCG:Adonor_gain0.9700
19:13774571:GGCGG:Gdonor_gain0.9700
19:13774747:T:TAdonor_gain0.9700

AlphaMissense

636 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:13778068:T:CI57T0.998
19:13778068:T:GI57S0.996
19:13774674:G:CK40N0.994
19:13774674:G:TK40N0.994
19:13778068:T:AI57N0.993
19:13774570:A:CK31N0.992
19:13774570:A:TK31N0.992
19:13778104:C:AA69D0.990
19:13778071:G:CR58P0.989
19:13778084:A:CE62D0.989
19:13778084:A:TE62D0.989
19:13774661:T:AI36N0.988
19:13774671:G:CK39N0.987
19:13774671:G:TK39N0.987
19:13778103:G:CA69P0.987
19:13774664:C:AA37D0.986
19:13778056:T:CL53P0.986
19:13774571:G:CG32R0.985
19:13774667:C:AP38H0.982
19:13774672:A:GK40E0.982
19:13774568:A:GK31E0.980
19:13774572:G:AG32D0.980
19:13774672:A:CK40Q0.980
19:13778083:A:TE62V0.980
19:13774567:A:CR30S0.978
19:13774567:A:TR30S0.978
19:13774571:G:TG32C0.978
19:13774487:G:AG4R0.975
19:13774487:G:CG4R0.975
19:13774488:G:AG4E0.975

dbSNP variants (sampled 300 via entrez): RS1000400241 (19:13774793 C>T), RS1000524220 (19:13779174 T>C), RS1000765052 (19:13776696 A>G), RS1000771175 (19:13774561 C>T), RS1001762923 (19:13775258 C>T), RS1001897230 (19:13775047 C>T), RS1001926366 (19:13776620 G>A), RS1001978960 (19:13776278 C>G,T), RS1002648121 (19:13774277 T>C), RS1002705993 (19:13778856 G>A), RS1003215287 (19:13778636 C>T), RS1003655034 (19:13775384 A>G,T), RS1003995239 (19:13778398 G>A,T), RS1004272163 (19:13774329 C>A,T), RS1004292151 (19:13773697 G>A)

Disease associations

OMIM: gene MIM:620685 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010703_143Brain morphology (MOSTest)5.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression2
triphenyl phosphateaffects expression1
methylparabendecreases expression1
cobaltous chloridedecreases expression1
CGP 52608affects binding, increases reaction1
chloropicrinincreases expression1
abrinedecreases expression1
Smokedecreases expression1
Aflatoxin B1increases expression1
Cadmium Chlorideincreases expression1
Particulate Matterdecreases expression1

Clinical trials (associated diseases)

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

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

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
v1.1.4
BioBTree
v2.0.2

Sources 73

This page pulls from 73 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot