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Atlas / Gene / CLDND2

CLDND2

gene
On this page

Also known as MGC33839

Summary

CLDND2 (claudin domain containing 2, HGNC:28511) is a protein-coding gene on chromosome 19q13.41, encoding Claudin domain-containing protein 2 (Q8NHS1).

Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 125875 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 33 total
  • MANE Select transcript: NM_152353

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28511
Approved symbolCLDND2
Nameclaudin domain containing 2
Location19q13.41
Locus typegene with protein product
StatusApproved
AliasesMGC33839
Ensembl geneENSG00000160318
Ensembl biotypeprotein_coding
Entrez125875

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000291715, ENST00000593841, ENST00000601435

RefSeq mRNA: 1 — MANE Select: NM_152353 NM_152353

CCDS: CCDS12829

Canonical transcript exons

ENST00000291715 — 4 exons

ExonStartEnd
ENSE000010514225136788651368026
ENSE000010514265136745751367576
ENSE000011252145136709851367215
ENSE000011873295136840951369003

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 95.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3381 / max 69.3453, expressed in 1375 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1823912.91351160
1823901.2312676
2089120.174175
1823920.01933

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047395.16silver quality
granulocyteCL:000009494.80gold quality
left testisUBERON:000453392.15gold quality
right testisUBERON:000453491.31gold quality
spermCL:000001989.39silver quality
testisUBERON:000047388.28gold quality
apex of heartUBERON:000209882.16gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099179.83gold quality
lower esophagus mucosaUBERON:003583477.40gold quality
mucosa of transverse colonUBERON:000499177.13gold quality
hypothalamusUBERON:000189877.12gold quality
anterior cingulate cortexUBERON:000983576.99gold quality
right lobe of liverUBERON:000111476.88gold quality
spleenUBERON:000210676.81gold quality
esophagogastric junction muscularis propriaUBERON:003584176.70gold quality
lower esophagus muscularis layerUBERON:003583376.46gold quality
lower esophagusUBERON:001347376.41gold quality
muscle layer of sigmoid colonUBERON:003580576.28gold quality
bloodUBERON:000017876.24gold quality
left adrenal gland cortexUBERON:003582576.24gold quality
amygdalaUBERON:000187675.78gold quality
right frontal lobeUBERON:000281075.71gold quality
right adrenal glandUBERON:000123375.51gold quality
left adrenal glandUBERON:000123475.50gold quality
Brodmann (1909) area 9UBERON:001354075.48gold quality
prefrontal cortexUBERON:000045175.17gold quality
left ovaryUBERON:000211974.97gold quality
right adrenal gland cortexUBERON:003582774.82gold quality
hindlimb stylopod muscleUBERON:000425274.76gold quality
right coronary arteryUBERON:000162574.74gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.27

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCldnd2ENSMUSG00000038973
rattus_norvegicusCldnd2ENSRNOG00000037333

Paralogs (10): LIM2 (ENSG00000105370), NKG7 (ENSG00000105374), PMP22 (ENSG00000109099), GSG1 (ENSG00000111305), EMP1 (ENSG00000134531), EMP3 (ENSG00000142227), GSG1L (ENSG00000169181), TMEM202 (ENSG00000187806), EMP2 (ENSG00000213853), GSG1L2 (ENSG00000214978)

Protein

Protein identifiers

Claudin domain-containing protein 2 — Q8NHS1 (reviewed: Q8NHS1)

All UniProt accessions (2): Q8NHS1, M0R1J6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the PMP-22/EMP/MP20 family.

RefSeq proteins (1): NP_689566* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004031PMP22/EMP/MP20/ClaudinFamily
IPR004032PMP22_EMP_MP20Family
IPR050579PMP-22/EMP/MP20-likeFamily

Pfam: PF00822

UniProt features (5 total): transmembrane region 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NHS1-F188.580.58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): GATA4_Q3, MIKKELSEN_ES_ICP_WITH_H3K4ME3, LU_EZH2_TARGETS_UP, FIGUEROA_AML_METHYLATION_CLUSTER_5_DN, SETD7_TARGET_GENES, SNRNP70_TARGET_GENES, ZNF513_TARGET_GENES, GSE10273_LOW_IL7_VS_HIGH_IL7_AND_IRF4_IN_IRF4_8_NULL_PRE_BCELL_DN, GSE7219_WT_VS_NIK_NFKB2_KO_DC_DN, MANNE_COVID19_NONICU_VS_HEALTHY_DONOR_PLATELETS_UP, MANNE_COVID19_COMBINED_COHORT_VS_HEALTHY_DONOR_PLATELETS_UP, TTCYRGAA_UNKNOWN, DESCARTES_FETAL_PLACENTA_LYMPHOID_CELLS, THAKAR_PBMC_INACTIVATED_INFLUENZA_AGE_21_30YO_RESPONDERS_28DY_DN, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL

GO Biological Process (0):

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

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLDND2MISP3Q96FF7592
CLDND2BPIFA3Q9BQP9466
CLDND2UQCC6Q69YU5437
CLDND2ANKRD39Q53RE8432
CLDND2CCDC102AQ96A19431
CLDND2SAXO4Q7Z5V6430
CLDND2BPIFA2Q96DR5415
CLDND2DHRS13Q6UX07399
CLDND2BPIFB4P59827397
CLDND2SCNM1Q9BWG6396
CLDND2RIPOR1Q6ZS17374
CLDND2TTC38Q5R3I4370
CLDND2NPEPL1Q8NDH3358
CLDND2ACTR8Q9H981351
CLDND2PANK4Q9NVE7329

IntAct

79 interactions, top by confidence:

ABTypeScore
CLDND2LHFPL5psi-mi:“MI:0915”(physical association)0.560
CLDND2ELOVL4psi-mi:“MI:0915”(physical association)0.560
CLDND2TMEM80psi-mi:“MI:0915”(physical association)0.560
CLDND2SAR1Apsi-mi:“MI:0915”(physical association)0.560
ANKRD13CCLDND2psi-mi:“MI:0915”(physical association)0.560
CLDND2psi-mi:“MI:0915”(physical association)0.560
BLCAPCLDND2psi-mi:“MI:0915”(physical association)0.560
AQP6CLDND2psi-mi:“MI:0915”(physical association)0.560
CLDND2REEP4psi-mi:“MI:0915”(physical association)0.560
FAM209ACLDND2psi-mi:“MI:0915”(physical association)0.560
CPLX4CLDND2psi-mi:“MI:0915”(physical association)0.560
CLDND2TMEM14Bpsi-mi:“MI:0915”(physical association)0.560
TMPPECLDND2psi-mi:“MI:0915”(physical association)0.560
CLDND2MTIF3psi-mi:“MI:0915”(physical association)0.560
EBPCLDND2psi-mi:“MI:0915”(physical association)0.560
GPR37L1CLDND2psi-mi:“MI:0915”(physical association)0.560
CLDND2GPR152psi-mi:“MI:0915”(physical association)0.560
RELL2CLDND2psi-mi:“MI:0915”(physical association)0.560
SLC10A6CLDND2psi-mi:“MI:0915”(physical association)0.560
MUC1CLDND2psi-mi:“MI:0915”(physical association)0.560
FFAR2CLDND2psi-mi:“MI:0915”(physical association)0.560
CLDND2FAM210Bpsi-mi:“MI:0915”(physical association)0.560
CLDND2ERGIC3psi-mi:“MI:0915”(physical association)0.560
GOLT1ACLDND2psi-mi:“MI:0915”(physical association)0.560

BioGRID (30): CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid), CLDND2 (Two-hybrid)

ESM2 similar proteins: A5A6N6, D3ZQJ0, F1QIK8, O09117, O35912, O88662, P19075, P47801, P54848, P54849, P54850, P54851, P54852, P56748, Q12999, Q16563, Q2NKU9, Q32KP1, Q3ZBY0, Q4KL25, Q58DR6, Q5PPI7, Q5R9S6, Q5RAI2, Q5RAP8, Q5RCY3, Q5U1V9, Q5XHG6, Q66HH2, Q66IV3, Q6DHB5, Q6GPN9, Q6P742, Q6Y1E2, Q6ZUX7, Q7ZUB3, Q7ZWW7, Q7ZZL8, Q8BGA2, Q8BI08

Diamond homologs: P20274, P54825, P55344, P56563, Q8NHS1, Q99PA5, Q9D9H2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance27
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

588 predictions. Top by Δscore:

VariantEffectΔscore
19:51367880:TCTCA:Tdonor_loss1.0000
19:51367881:CTCA:Cdonor_loss1.0000
19:51367882:TCA:Tdonor_loss1.0000
19:51367883:CACC:Cdonor_loss1.0000
19:51367884:A:ACdonor_gain1.0000
19:51367884:A:ATdonor_loss1.0000
19:51367884:ACCG:Adonor_gain1.0000
19:51367885:C:CCdonor_gain1.0000
19:51367885:C:CGdonor_loss1.0000
19:51367885:CCG:Cdonor_gain1.0000
19:51367885:CCGC:Cdonor_gain1.0000
19:51367854:G:Adonor_gain0.9900
19:51367862:G:Adonor_gain0.9900
19:51367932:G:Adonor_gain0.9900
19:51367113:T:Adonor_gain0.9800
19:51367490:C:Tacceptor_gain0.9800
19:51368027:C:CCacceptor_gain0.9800
19:51367490:C:CTacceptor_gain0.9700
19:51367491:A:Tacceptor_gain0.9700
19:51367858:G:Adonor_gain0.9700
19:51368408:CT:Cdonor_gain0.9600
19:51367458:C:CTacceptor_gain0.9500
19:51367881:CT:Cdonor_loss0.9500
19:51368022:CGTGG:Cacceptor_gain0.9500
19:51367504:C:CTacceptor_gain0.9400
19:51367850:C:Adonor_gain0.9400
19:51367879:GTCT:Gdonor_loss0.9400
19:51367458:C:Tacceptor_gain0.9300
19:51367884:ACCGC:Adonor_gain0.9300
19:51367885:CCGCC:Cdonor_gain0.9300

AlphaMissense

1079 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:51367487:A:GW134R0.973
19:51367487:A:TW134R0.973
19:51367157:G:CF163L0.955
19:51367157:G:TF163L0.955
19:51367159:A:GF163L0.955
19:51367505:A:GW128R0.952
19:51367505:A:TW128R0.952
19:51368485:C:AW31C0.945
19:51368485:C:GW31C0.945
19:51368487:A:GW31R0.937
19:51368487:A:TW31R0.937
19:51367457:C:GG144R0.936
19:51367215:C:TG144D0.921
19:51367501:G:AS129F0.921
19:51367509:G:CF126L0.921
19:51367509:G:TF126L0.921
19:51367511:A:GF126L0.921
19:51367886:C:GG104R0.916
19:51367886:C:TG104R0.916
19:51367499:A:CY130D0.913
19:51367205:A:CF147L0.902
19:51367205:A:TF147L0.902
19:51367207:A:GF147L0.902
19:51367210:A:GC146R0.896
19:51368495:G:AT28I0.895
19:51367489:C:TG133E0.892
19:51367480:G:TA136D0.890
19:51367474:G:CP138R0.889
19:51368452:C:AW42C0.888
19:51368452:C:GW42C0.888

dbSNP variants (sampled 300 via entrez): RS1002323217 (19:51366731 T>A,G), RS1002963012 (19:51368782 C>A,G,T), RS1004336890 (19:51369261 G>A), RS1004369396 (19:51369003 C>CG), RS1004475309 (19:51369144 G>A,C,T), RS1005861978 (19:51369975 G>A,C), RS1006990223 (19:51370921 G>A), RS1007943211 (19:51366890 C>T), RS1008767136 (19:51367695 C>A,G,T), RS1008931827 (19:51369830 C>T), RS1009321962 (19:51366931 C>T), RS1010010624 (19:51370965 C>T), RS1010332986 (19:51368113 C>A), RS1010821340 (19:51366551 G>A,C,T), RS1011056672 (19:51369648 G>T)

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

1 associations (top):

StudyTraitp-value
GCST009391_1417Metabolite levels5.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010452adenosine diphosphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Saffects cotreatment, increases expression2
Valproic Aciddecreases expression, increases methylation2
bisphenol Faffects cotreatment, increases expression1
kojic aciddecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
Acetaminophendecreases expression1
Atrazineincreases expression1
Benzo(a)pyrenedecreases methylation1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Testosteroneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Asbestos, Serpentinedecreases methylation1
Lactic Acidincreases 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 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