DGCR6L

gene
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Also known as FLJ10666

Summary

DGCR6L (DiGeorge syndrome critical region gene 6 like, HGNC:18551) is a protein-coding gene on chromosome 22q11.21, encoding Protein DGCR6L (Q9BY27). May play a role in neural crest cell migration into the third and fourth pharyngeal pouches.

This gene, the result of a duplication at this locus, is one of two functional genes encoding nearly identical proteins that have similar expression patterns. The product of this gene is a protein that shares homology with the Drosophila gonadal protein, expressed in gonadal tissues and germ cells, and with the human laminin gamma-1 chain that functions in cell attachment and migration. This gene is located in a region of chromosome 22 implicated in the DiGeorge syndrome, one facet of a broader collection of anomalies referred to as the CATCH 22 syndrome.

Source: NCBI Gene 85359 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 47 total — 1 pathogenic
  • MANE Select transcript: NM_033257

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18551
Approved symbolDGCR6L
NameDiGeorge syndrome critical region gene 6 like
Location22q11.21
Locus typegene with protein product
StatusApproved
AliasesFLJ10666
Ensembl geneENSG00000128185
Ensembl biotypeprotein_coding
OMIM609459
Entrez85359

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 nonsense_mediated_decay

ENST00000248879, ENST00000405465, ENST00000443409, ENST00000875445, ENST00000911281, ENST00000911282, ENST00000911283, ENST00000911284, ENST00000911285, ENST00000911286

RefSeq mRNA: 1 — MANE Select: NM_033257 NM_033257

CCDS: CCDS13778

Canonical transcript exons

ENST00000248879 — 5 exons

ExonStartEnd
ENSE000015997852031611920316219
ENSE000017313922031963920319799
ENSE000018558552031423820314824
ENSE000036741762031533620315476
ENSE000038898782031987920320060

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 97.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.4948 / max 87.8434, expressed in 1799 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
19319117.49481799

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453497.97gold quality
left testisUBERON:000453397.79gold quality
testisUBERON:000047397.30gold quality
right lobe of liverUBERON:000111496.82gold quality
apex of heartUBERON:000209896.01gold quality
amygdalaUBERON:000187695.69gold quality
temporal lobeUBERON:000187195.66gold quality
putamenUBERON:000187495.63gold quality
nucleus accumbensUBERON:000188295.39gold quality
anterior cingulate cortexUBERON:000983595.20gold quality
caudate nucleusUBERON:000187395.13gold quality
Ammon’s hornUBERON:000195495.13gold quality
hindlimb stylopod muscleUBERON:000425295.12gold quality
dorsolateral prefrontal cortexUBERON:000983494.80gold quality
Brodmann (1909) area 9UBERON:001354094.73gold quality
right frontal lobeUBERON:000281094.67gold quality
hypothalamusUBERON:000189894.64gold quality
cerebral cortexUBERON:000095694.53gold quality
substantia nigraUBERON:000203894.51gold quality
liverUBERON:000210794.39gold quality
prefrontal cortexUBERON:000045194.28gold quality
frontal cortexUBERON:000187094.28gold quality
gastrocnemiusUBERON:000138894.27gold quality
muscle of legUBERON:000138393.84gold quality
heart left ventricleUBERON:000208493.80gold quality
brainUBERON:000095593.66gold quality
adult mammalian kidneyUBERON:000008293.57gold quality
primary visual cortexUBERON:000243693.50gold quality
spinal cordUBERON:000224093.44gold quality
C1 segment of cervical spinal cordUBERON:000646993.44gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-CURD-112no3.61
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting DGCR6L, 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-4649-3P99.5666.901783
HSA-MIR-392698.9569.261438
HSA-MIR-1301-3P98.6468.271071
HSA-MIR-296-5P97.6164.02851
HSA-MIR-4640-5P97.4266.331543
HSA-MIR-6508-3P96.7365.48576
HSA-MIR-397496.5666.22928
HSA-MIR-3677-5P93.1664.62393

Literature-anchored findings (GeneRIF, showing 2)

  • DGCR6L, a novel PAK4 interacting protein, regulated PAK4-mediated migration of human gastric cancer cells via LIMK1. (PMID:19778628)
  • Further studies are now needed to test the usefulness of DGCR6 and DGCR6L expression and alterations in the epigenome at these loci in predicting childhood anxiety and associated adult-onset pathologies in 22q11DS subjects. (PMID:22832905)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriodgcr6ENSDARG00000005500
mus_musculusDgcr6ENSMUSG00000003531
rattus_norvegicusDgcr6ENSRNOG00000001880
drosophila_melanogastergdlFBGN0001099

Paralogs (2): DGCR6 (ENSG00000183628), (ENSG00000278817)

Protein

Protein identifiers

Protein DGCR6LQ9BY27 (reviewed: Q9BY27)

Alternative names: DiGeorge syndrome critical region 6-like protein

All UniProt accessions (3): Q9BY27, B5MCQ4, F8WCX1

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in neural crest cell migration into the third and fourth pharyngeal pouches.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed in fetal and adult tissues. Highest expression in liver, heart and skeletal muscle. Lower levels in pancreas and placenta. Weak expression in brain.

Similarity. Belongs to the gonadal family.

RefSeq proteins (1): NP_150282* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010849GonadalFamily

Pfam: PF07324

UniProt features (6 total): sequence variant 2, sequence conflict 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BY27-F187.100.72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): JIANG_VHL_TARGETS, JIANG_HYPOXIA_VIA_VHL, KRAS.600.LUNG.BREAST_UP.V1_DN, GUCY1B1_TARGET_GENES, MAFG_TARGET_GENES, NFE2L1_TARGET_GENES, TASOR_TARGET_GENES, SAFB2_TARGET_GENES, WP_22Q112_COPY_NUMBER_VARIATION_SYNDROME, DESCARTES_MAIN_FETAL_AFP_ALB_POSITIVE_CELLS, DESCARTES_FETAL_HEART_ERYTHROBLASTS, DESCARTES_FETAL_SPLEEN_AFP_ALB_POSITIVE_CELLS, SETBP1_TARGET_GENES, LOPEZ_MBD_TARGETS, TRAVAGLINI_LUNG_PROXIMAL_CILIATED_CELL

GO Biological Process (0):

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

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

560 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DGCR6LPRODHO43272884
DGCR6LZNF74Q16587841
DGCR6LDGCR2P98153831
DGCR6LPRODHO43272796
DGCR6LHIRAP54198756
DGCR6LSERPIND1P05546716
DGCR6LTBX1O43435705
DGCR6LGNB1LQ9BYB4684
DGCR6LPAK4O96013665
DGCR6LCOMTP21964612
DGCR6LGSC2O15499596
DGCR6LZDHHC8Q9ULC8581
DGCR6LUFD1Q92890571
DGCR6LMRPL40Q9NQ50537
DGCR6LZNF490Q9ULM2490

IntAct

87 interactions, top by confidence:

ABTypeScore
DEUP1DGCR6Lpsi-mi:“MI:0915”(physical association)0.720
MID2DGCR6Lpsi-mi:“MI:0915”(physical association)0.720
DGCR6LDEUP1psi-mi:“MI:0915”(physical association)0.720
DGCR6LMID2psi-mi:“MI:0915”(physical association)0.720
DGCR6LINIPpsi-mi:“MI:0915”(physical association)0.600
INIPDGCR6Lpsi-mi:“MI:0915”(physical association)0.600
KRT31DGCR6Lpsi-mi:“MI:0915”(physical association)0.560
DGCR6LLZTS2psi-mi:“MI:0915”(physical association)0.560
DGCR6LRIMBP3psi-mi:“MI:0915”(physical association)0.560
LZTS2DGCR6Lpsi-mi:“MI:0915”(physical association)0.560
DGCR6LKRT31psi-mi:“MI:0915”(physical association)0.560
DGCR6LZNF620psi-mi:“MI:0915”(physical association)0.560
PPP1R13BDGCR6Lpsi-mi:“MI:0915”(physical association)0.560
NAB2DGCR6Lpsi-mi:“MI:0915”(physical association)0.560
GATA1DGCR6Lpsi-mi:“MI:0915”(physical association)0.560
SPTA1DGCR6Lpsi-mi:“MI:0915”(physical association)0.560
ADAMTSL4DGCR6Lpsi-mi:“MI:0915”(physical association)0.560
NECAB2DGCR6Lpsi-mi:“MI:0915”(physical association)0.560

BioGRID (36): DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), RIMBP3 (Two-hybrid), CCDC67 (Two-hybrid), DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), KCNRG (Two-hybrid), DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), DGCR6L (Two-hybrid), PAK4 (Reconstituted Complex), DGCR6L (Reconstituted Complex)

ESM2 similar proteins: A1IGU3, A1IGU4, A1IGU5, A5D8V7, A5PK16, A6QP29, A7E3N7, A8K8P3, A9CB34, B0KWR6, B5DFA1, D3ZI76, G3HQ82, O73770, P0C7M6, P41002, Q14129, Q14DK4, Q15051, Q3SYS7, Q3UK37, Q3UZY0, Q5SNV9, Q5SXM2, Q60953, Q60I26, Q60I27, Q69ZT1, Q6NUI2, Q8BP00, Q8BP86, Q8C1F5, Q8C2K1, Q8CJ00, Q8IV45, Q8NCU4, Q8NE28, Q8NEE8, Q8TE82, Q95KD7

Diamond homologs: O35347, O73770, P22468, Q14129, Q9BY27

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance34
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
666443GRCh37/hg19 22q11.21(chr22:18661724-21505417)x1Pathogenic

SpliceAI

860 predictions. Top by Δscore:

VariantEffectΔscore
22:20315332:TGACC:Tdonor_loss1.0000
22:20315333:GACCT:Gdonor_loss1.0000
22:20315334:A:ACdonor_gain1.0000
22:20315335:C:CCdonor_gain1.0000
22:20315473:CGGC:Cacceptor_gain1.0000
22:20315474:GGC:Gacceptor_gain1.0000
22:20315475:GC:Gacceptor_gain1.0000
22:20315475:GCCT:Gacceptor_loss1.0000
22:20315476:CC:Cacceptor_gain1.0000
22:20315477:C:Aacceptor_loss1.0000
22:20315477:C:CCacceptor_gain1.0000
22:20315481:C:CTacceptor_gain1.0000
22:20315481:C:Tacceptor_gain1.0000
22:20315482:A:Cacceptor_gain1.0000
22:20315489:C:CTacceptor_gain1.0000
22:20315489:C:Tacceptor_gain1.0000
22:20315490:A:Tacceptor_gain1.0000
22:20315494:C:CTacceptor_gain1.0000
22:20315496:C:CTacceptor_gain1.0000
22:20316217:GCA:Gacceptor_gain1.0000
22:20316218:CA:Cacceptor_gain1.0000
22:20316218:CAC:Cacceptor_gain1.0000
22:20316220:C:CCacceptor_gain1.0000
22:20319874:CGTA:Cdonor_loss1.0000
22:20319875:GTACC:Gdonor_loss1.0000
22:20319876:TA:Tdonor_loss1.0000
22:20319877:A:ATdonor_loss1.0000
22:20315334:AC:Adonor_gain0.9900
22:20315335:CC:Cdonor_gain0.9900
22:20315472:ACGGC:Aacceptor_gain0.9900

AlphaMissense

1404 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:20315357:G:CF164L0.996
22:20315357:G:TF164L0.996
22:20315359:A:GF164L0.996
22:20315390:C:AQ153H0.996
22:20315390:C:GQ153H0.996
22:20319710:A:GL67P0.995
22:20315358:A:GF164S0.994
22:20319692:A:GL73P0.994
22:20319722:A:CI63S0.994
22:20319755:G:TA52D0.994
22:20315382:A:GL156P0.993
22:20319697:C:AQ71H0.992
22:20319697:C:GQ71H0.992
22:20319758:A:GL51P0.992
22:20315415:A:GL145P0.991
22:20319665:C:GR82P0.991
22:20314793:A:GL182P0.990
22:20315393:C:AQ152H0.990
22:20315393:C:GQ152H0.990
22:20315382:A:TL156Q0.989
22:20319677:A:GL78P0.989
22:20319685:T:AE75D0.989
22:20319685:T:GE75D0.989
22:20319722:A:TI63N0.989
22:20319746:A:TL55H0.989
22:20314802:A:GL179P0.988
22:20315349:G:AT167I0.988
22:20319722:A:GI63T0.988
22:20319746:A:GL55P0.988
22:20319701:A:GI70T0.986

dbSNP variants (sampled 300 via entrez): RS1000069961 (22:20315902 C>T), RS1000111803 (22:20316787 A>G), RS1001668014 (22:20318454 T>C), RS1001782404 (22:20318024 C>T), RS1003682701 (22:20320934 TG>T), RS1003714034 (22:20320770 C>T), RS1004050868 (22:20321966 G>A,T), RS1005932348 (22:20317927 G>A), RS1007245094 (22:20314492 C>T), RS1007519424 (22:20320475 G>A), RS1007818623 (22:20321773 T>G), RS1007852966 (22:20321582 G>T), RS1007944915 (22:20320719 G>C,T), RS1008503636 (22:20315950 G>A,T), RS1008887364 (22:20316155 C>T)

Disease associations

OMIM: gene MIM:609459 | disease phenotypes: MIM:188400, MIM:192430

GenCC curated gene-disease

Mondo (4): prostate cancer (MONDO:0008315), primary ovarian failure (MONDO:0005387), DiGeorge syndrome (MONDO:0008564), velocardiofacial syndrome (MONDO:0008644)

Orphanet (3): Familial prostate cancer (Orphanet:1331), 22q11.2 deletion syndrome (Orphanet:567), NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (3)

DescriptorNameTree numbers
D004062DiGeorge SyndromeC05.660.207.103.500; C14.240.400.021.500; C14.280.400.044.500; C15.604.451.249.500; C16.131.077.019.500; C16.131.240.400.021.500; C16.131.260.019.500; C16.131.482.249.500; C16.131.621.207.103.500; C16.320.180.019.500; C19.642.482.500.500
D016649Primary Ovarian InsufficiencyC12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750
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

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
Cisplatinaffects cotreatment, increases expression2
aristolochic acid Iincreases expression1
bisphenol Aaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicinaffects expression1
Indomethacinincreases expression, affects cotreatment1
Smokedecreases expression1
Thiramdecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Copper Sulfatedecreases expression1
Acrylamidedecreases expression1
Vitamin K 3affects 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