KLHDC7B

gene
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Also known as MGC16635

Summary

KLHDC7B (kelch domain containing 7B, HGNC:25145) is a protein-coding gene on chromosome 22q13.33, encoding Kelch domain-containing protein 7B (Q96G42).

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 124 total — 2 pathogenic
  • MANE Select transcript: NM_138433

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25145
Approved symbolKLHDC7B
Namekelch domain containing 7B
Location22q13.33
Locus typegene with protein product
StatusApproved
AliasesMGC16635
Ensembl geneENSG00000130487
Ensembl biotypeprotein_coding
OMIM620521
Entrez113730

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000434237, ENST00000648057

RefSeq mRNA: 1 — MANE Select: NM_138433 NM_138433

CCDS: CCDS14097

Canonical transcript exons

ENST00000648057 — 1 exons

ExonStartEnd
ENSE000038406065054589950551023

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 81.94.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7847 / max 165.7375, expressed in 439 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1930250.9076213
1930280.4399123
1930230.195779
1930260.111739
1930240.073635
1930270.056325

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
palpebral conjunctivaUBERON:000181281.94gold quality
granulocyteCL:000009478.62gold quality
mucosa of paranasal sinusUBERON:000503078.20silver quality
epithelium of nasopharynxUBERON:000195178.04gold quality
pancreatic ductal cellCL:000207975.79silver quality
kidney epitheliumUBERON:000481975.36gold quality
nasal cavity epitheliumUBERON:000538473.92gold quality
leukocyteCL:000073872.51gold quality
monocyteCL:000057671.98gold quality
cardiac muscle of right atriumUBERON:000337970.80gold quality
left ventricle myocardiumUBERON:000656670.45gold quality
ileal mucosaUBERON:000033170.12silver quality
superficial temporal arteryUBERON:000161470.12gold quality
thymusUBERON:000237069.03gold quality
bloodUBERON:000017868.63gold quality
vermiform appendixUBERON:000115466.38gold quality
olfactory segment of nasal mucosaUBERON:000538666.25gold quality
nasal cavity mucosaUBERON:000182665.93gold quality
spleenUBERON:000210665.61gold quality
bone marrow cellCL:000209265.59silver quality
lymph nodeUBERON:000002964.89gold quality
tibialis anteriorUBERON:000138564.06silver quality
caecumUBERON:000115361.83gold quality
bone marrowUBERON:000237160.50gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450259.59gold quality
myocardiumUBERON:000234958.99gold quality
lower lobe of lungUBERON:000894958.98silver quality
amniotic fluidUBERON:000017358.37silver quality
esophagus squamous epitheliumUBERON:000692058.24silver quality
tracheaUBERON:000312656.98silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting KLHDC7B, 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-990299.8969.152250
HSA-MIR-449299.8768.253611
HSA-MIR-317599.6566.302031
HSA-MIR-486-3P99.5166.821901
HSA-MIR-468899.4864.68828
HSA-MIR-6743-5P99.4863.60721
HSA-MIR-449899.4767.422360
HSA-MIR-7113-3P98.7565.711120
HSA-MIR-19898.7067.32920
HSA-MIR-423-5P98.6967.481522
HSA-MIR-3184-5P98.5667.131491
HSA-MIR-317998.2265.901445
HSA-MIR-6893-3P97.7964.911238
HSA-MIR-3085-5P97.7265.43544
HSA-MIR-376C-3P97.6368.881263
HSA-MIR-430897.5667.131385
HSA-MIR-1225-3P97.2964.60876
HSA-MIR-370-3P97.0964.921221
HSA-MIR-390796.7665.04662
HSA-MIR-7160-3P96.4064.15462
HSA-MIR-381-5P91.9165.0365

Literature-anchored findings (GeneRIF, showing 3)

  • Hs.137007 gene is a novel gene specifically expressed in the breast that has a role in epigenetic regulation of breast cancer [Hs.137007] (PMID:20372783)
  • HPV E7 affects the function of cervical cancer cells via the TAL1/lncEBIC/KLHDC7B axis. (PMID:33760214)
  • KLHDC7B as a novel diagnostic biomarker in urine exosomal mRNA promotes bladder urothelial carcinoma cell proliferation and migration, inhibits apoptosis. (PMID:37888201)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusKlhdc7bENSMUSG00000091680
rattus_norvegicusKlhdc7bENSRNOG00000032419

Paralogs (54): KLHL13 (ENSG00000003096), KLHL20 (ENSG00000076321), KEAP1 (ENSG00000079999), KLHL42 (ENSG00000087448), KLHL22 (ENSG00000099910), KLHL4 (ENSG00000102271), KLHL2 (ENSG00000109466), KLHL5 (ENSG00000109790), BACH2 (ENSG00000112182), KLHL18 (ENSG00000114648), KLHL24 (ENSG00000114796), IVNS1ABP (ENSG00000116679), KLHL12 (ENSG00000117153), KLHL29 (ENSG00000119771), KBTBD7 (ENSG00000120696), KLHL7 (ENSG00000122550), KLHL31 (ENSG00000124743), KLHL36 (ENSG00000135686), KLHL8 (ENSG00000145332), KLHL3 (ENSG00000146021), KLHL35 (ENSG00000149243), KLHL1 (ENSG00000150361), BACH1 (ENSG00000156273), KLHL40 (ENSG00000157119), KLHL10 (ENSG00000161594), KLHL21 (ENSG00000162413), KLHDC8A (ENSG00000162873), KBTBD8 (ENSG00000163376), KBTBD6 (ENSG00000165572), KLHL26 (ENSG00000167487), KLHL30 (ENSG00000168427), KBTBD2 (ENSG00000170852), KLHL6 (ENSG00000172578), KLHL15 (ENSG00000174010), KLHL38 (ENSG00000175946), KBTBD11 (ENSG00000176595), KLHDC7A (ENSG00000179023), KLHL28 (ENSG00000179454), KBTBD3 (ENSG00000182359), KLHL33 (ENSG00000185271)

Protein

Protein identifiers

Kelch domain-containing protein 7BQ96G42 (reviewed: Q96G42)

All UniProt accessions (1): A0A3B3ISF6

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_612442* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006652Kelch_1Repeat
IPR015915Kelch-typ_b-propellerHomologous_superfamily
IPR052310Kelch/BTB_domain_proteinFamily

Pfam: PF01344

UniProt features (11 total): repeat 5, compositionally biased region 4, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96G42-F169.930.42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): chr22q13, WANG_SMARCE1_TARGETS_UP, RICKMAN_HEAD_AND_NECK_CANCER_F, MIR376C_3P, MIR3179, GSE13485_CTRL_VS_DAY3_YF17D_VACCINE_PBMC_DN, GSE13485_CTRL_VS_DAY7_YF17D_VACCINE_PBMC_DN, GSE13485_DAY1_VS_DAY7_YF17D_VACCINE_PBMC_DN, GSE13485_DAY3_VS_DAY7_YF17D_VACCINE_PBMC_DN, GSE13485_PRE_VS_POST_YF17D_VACCINATION_PBMC_DN, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_CALU3_CELLS_UP, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_UP, NAKAYAMA_FRA2_TARGETS, GAO_LARGE_INTESTINE_24W_C11_PANETH_LIKE_CELL, ZAK_PBMC_MRKAD5_HIV_1_GAG_POL_NEF_AGE_20_50YO_1DY_UP

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1

Protein interactions and networks

STRING

386 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KLHDC7BCLRN2A0PK11490
KLHDC7BOR4F21O95013417
KLHDC7BZNF487B1APH4400
KLHDC7BGARIN5AQ6IPT2393
KLHDC7BFSCN2O14926359
KLHDC7BTRABDQ9H4I3339
KLHDC7BCCDC68Q9H2F9334
KLHDC7BSYNJ2O15056326
KLHDC7BCIB4A0PJX0321
KLHDC7BEVA1BQ9NVM1316
KLHDC7BRNF208Q9H0X6316
KLHDC7BTRIOBPQ9H2D6311
KLHDC7BSHCBP1LQ9BZQ2301
KLHDC7BBAIAP2L2Q6UXY1300
KLHDC7BDENND6BQ8NEG7300

IntAct

73 interactions, top by confidence:

ABTypeScore
KLHDC7BMAPRE3psi-mi:“MI:0915”(physical association)0.560
KLHDC7BHNRNPUL1psi-mi:“MI:0915”(physical association)0.560
FNDC3BKLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
TBX6KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
KLHDC7BA1CFpsi-mi:“MI:0915”(physical association)0.560
SMUG1KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
BHLHE40KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
KLHDC7BPATZ1psi-mi:“MI:0915”(physical association)0.560
ESRP1KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
PHC2KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
RBPMSKLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
NFYCKLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
KLHDC7BSPMIP9psi-mi:“MI:0915”(physical association)0.560
KLHDC7BWWOXpsi-mi:“MI:0915”(physical association)0.560
TP53BP1KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
RBPMS2KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
KLHDC7BRHOXF2psi-mi:“MI:0915”(physical association)0.560
KLHDC7BZC3H10psi-mi:“MI:0915”(physical association)0.560
QRICH1KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
DTX2KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
LIMS4KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
POGZKLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
TLE5KLHDC7Bpsi-mi:“MI:0915”(physical association)0.560
NUDCD3KLHDC7Bpsi-mi:“MI:0915”(physical association)0.400
CFTRKLHDC7Bpsi-mi:“MI:0915”(physical association)0.370
EPHB6PGRMC1psi-mi:“MI:0914”(association)0.350
MAPRE3KLHDC7Bpsi-mi:“MI:0915”(physical association)0.000
HNRNPUL1KLHDC7Bpsi-mi:“MI:0915”(physical association)0.000

BioGRID (27): KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), KLHDC7B (Two-hybrid), RHOXF2 (Two-hybrid), BHLHE40 (Two-hybrid), PHC2 (Two-hybrid), ZC3H10 (Two-hybrid), POGZ (Two-hybrid)

ESM2 similar proteins: A1L3C1, A2AWP8, A2RRU4, A6QM06, A6QNS9, E1BBQ2, F1LQY6, G3V9M2, O43189, O94827, P29372, P29590, P41155, P97260, Q01113, Q02833, Q04841, Q0P5I0, Q12770, Q13387, Q13505, Q29RM4, Q32L49, Q3V1H9, Q5MNU5, Q5R5M3, Q66T02, Q69Z89, Q6GQT6, Q6IPT2, Q6RFZ7, Q6ZN54, Q70EL4, Q7Z6G3, Q8BQB4, Q8C4U2, Q8N1F8, Q8N554, Q8WWW0, Q8WXF8

Diamond homologs: A0JN76, A1L4W5, A2AAX3, B1WBS3, B2RXF5, B7U179, D3YUB6, D3ZA50, O14867, O15062, O43167, P0DMR5, P0DMR6, P41182, P41183, P97303, Q0IJ29, Q13105, Q1L8W0, Q24174, Q3B725, Q3B7N9, Q52KB5, Q5EXX3, Q5R4Q7, Q5R4S6, Q5R5N5, Q5RGB8, Q5ZJU2, Q5ZM39, Q60821, Q6DDV0, Q6DEL7, Q6NRM8, Q6P882, Q6P8B3, Q6YCH1, Q6YCH2, Q6ZSB9, Q717B2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance106
Likely benign16
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
154200GRCh38/hg38 22q13.33(chr22:50485457-50759410)x1Pathogenic
976871NC_000022.11:g.48500337_50739785delPathogenic

SpliceAI

38 predictions. Top by Δscore:

VariantEffectΔscore
22:50550751:A:AGacceptor_gain0.7700
22:50550752:A:Gacceptor_gain0.7600
22:50548599:G:GTdonor_gain0.5800
22:50550755:T:Gacceptor_gain0.5600
22:50550750:T:Gacceptor_gain0.5400
22:50550751:AAAAT:Aacceptor_gain0.5200
22:50548837:TG:Tacceptor_gain0.4900
22:50548838:GG:Gacceptor_gain0.4900
22:50549992:G:GTdonor_gain0.4800
22:50548099:A:Tdonor_gain0.4400
22:50550757:T:TAacceptor_gain0.4300
22:50548197:C:Tdonor_gain0.3900
22:50548213:G:GTdonor_gain0.3300
22:50549705:A:AGdonor_gain0.3100
22:50549706:G:GGdonor_gain0.3100
22:50548604:C:Adonor_gain0.3000
22:50550762:A:AGacceptor_gain0.3000
22:50550763:G:GGacceptor_gain0.3000
22:50549727:G:Tdonor_gain0.2900
22:50550753:AATGT:Aacceptor_gain0.2900
22:50550753:A:AGacceptor_gain0.2600
22:50548408:GCC:Gdonor_gain0.2500
22:50548834:G:GAacceptor_gain0.2500
22:50550754:ATGT:Aacceptor_gain0.2500
22:50548134:C:Tdonor_gain0.2400
22:50550758:G:Aacceptor_gain0.2400
22:50548574:C:Adonor_gain0.2300
22:50549726:G:GTdonor_gain0.2200
22:50549780:C:CTacceptor_gain0.2200
22:50550749:A:AGacceptor_gain0.2200

AlphaMissense

7745 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:50549448:T:AW428R0.997
22:50549448:T:CW428R0.997
22:50549527:T:AV454D0.997
22:50549450:G:CW428C0.996
22:50549450:G:TW428C0.996
22:50549481:T:CF439L0.995
22:50549483:C:AF439L0.995
22:50549483:C:GF439L0.995
22:50549583:T:AW473R0.995
22:50549583:T:CW473R0.995
22:50549585:G:CW473C0.995
22:50549585:G:TW473C0.995
22:50549319:T:AW385R0.994
22:50549319:T:CW385R0.994
22:50549697:T:GY511D0.994
22:50549718:T:AW518R0.994
22:50549718:T:CW518R0.994
22:50549236:T:CF357S0.992
22:50549562:T:GY466D0.992
22:50549659:T:CF498S0.992
22:50549392:C:AA409D0.991
22:50549658:T:CF498L0.991
22:50549660:C:AF498L0.991
22:50549660:C:GF498L0.991
22:50549160:T:AW332R0.989
22:50549160:T:CW332R0.989
22:50549401:G:TG412V0.989
22:50549652:T:GY496D0.989
22:50549720:G:CW518C0.989
22:50549720:G:TW518C0.989

dbSNP variants (sampled 300 via entrez): RS1000775439 (22:50550655 G>A), RS1000841692 (22:50547283 G>A,T), RS1000920445 (22:50547504 T>C), RS1000989632 (22:50545082 C>T), RS1001340166 (22:50544786 C>A,T), RS1001692560 (22:50548084 G>A,T), RS1001723562 (22:50548443 G>A,C), RS1001724708 (22:50546430 G>A,C), RS1002026267 (22:50546905 C>G,T), RS1002496754 (22:50550890 C>A,T), RS1002843338 (22:50548356 C>G,T), RS1003246485 (22:50549207 C>A,T), RS1003367112 (22:50547747 C>T), RS1003696261 (22:50545713 C>G,T), RS1004132385 (22:50545985 AGCTGGTGGG>A)

Disease associations

OMIM: gene MIM:620521 | disease phenotypes: MIM:606232

GenCC curated gene-disease

Mondo (1): Phelan-McDermid syndrome (MONDO:0011652)

Orphanet (1): Phelan-McDermid syndrome (Orphanet:48652)

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST000587_8Mean corpuscular hemoglobin4.000000e-08
GCST005996_9Red blood cell count4.000000e-10
GCST012020_516Serum metabolite levels4.000000e-23
GCST012442_12Age-related hearing impairment2.000000e-29
GCST012442_26Age-related hearing impairment3.000000e-10
GCST90002393_596Monocyte count3.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004509hemoglobin measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0004305erythrocyte count
EFO:0005091monocyte count

MeSH disease descriptors (1)

DescriptorNameTree numbers
C536801Telomeric 22q13 Monosomy Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression4
bisphenol Aaffects expression, increases expression2
Cyclosporineincreases expression2
GSK-J4decreases expression1
sotorasibaffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
hydroxyhydroquinonedecreases reaction, increases expression1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydeincreases expression1
perfluorooctanoic acidincreases expression1
ferrous chloridedecreases expression1
4-aminobenzhydrazideincreases expression, decreases reaction1
di-n-butylphosphoric acidaffects expression1
abrineincreases expression1
NSC 689534affects binding, increases expression1
trametinibaffects cotreatment, increases expression1
NVP-BKM120affects cotreatment, increases expression1
Bortezomibincreases expression1
Resveratroldecreases expression, affects cotreatment1
Sunitinibincreases expression1
Microplasticsaffects expression, increases abundance1
Benzo(a)pyreneaffects methylation, decreases methylation1
Calcitriolincreases expression1
Cisplatindecreases expression1
Copperaffects binding, increases expression1
Dexamethasonedecreases expression1
Formaldehydedecreases expression1
Ironincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT07281079PHASE3RECRUITINGA Study of NNZ-2591 in Pediatric Participants With Phelan-McDermid Syndrome
NCT07593391PHASE3RECRUITINGAn Open-label Study of NNZ-2591 in Pediatric Participants With Phelan-McDermid Syndrome
NCT01525901PHASE2COMPLETEDClinical Trial in 22q13 Deletion Syndrome(Phelan-McDermid Syndrome)
NCT02710084PHASE2COMPLETEDPiloting Treatment With Intranasal Oxytocin in Phelan-McDermid Syndrome
NCT03493607PHASE2COMPLETEDAMO-01 to Treat Adolescents and Adults With Phelan-McDermid Syndrome (PMS) and Co-morbid Epilepsy
NCT04003207PHASE2COMPLETEDGrowth Hormone Treatment in Children With Phelan McDermid Syndrome
NCT05025241PHASE2COMPLETEDAn Open-Label Study of Oral NNZ-2591 in Phelan-McDermid Syndrome (PMS-001)
NCT05187377PHASE2COMPLETEDA Controlled Trial of Growth Hormone in Phelan-McDermid Syndrome and Idiopathic Autism
NCT05105685PHASE1/PHASE2COMPLETEDEffectiveness of Recombinant Human Growth Hormone Therapy for Children With PMS
NCT06662188PHASE1/PHASE2RECRUITINGJAG201 Gene Therapy Study in Children & Adults With SHANK3 Haploinsufficiency
NCT02000167Not specifiedCOMPLETEDMitochondrial Dysfunction in Phelan-McDermid Syndrome
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT03426059Not specifiedCOMPLETEDMapping the Phenotype in Adults With Phelan-McDermid Syndrome
NCT03836300Not specifiedENROLLING_BY_INVITATIONParent and Infant Inter(X)Action Intervention (PIXI)
NCT04312152Not specifiedUNKNOWNQ10 Ubiquinol in Autism Spectrum Disorder and in Phelan-McDermid Syndrome.
NCT07014020Not specifiedRECRUITINGRB001 Gene Therapy Study in Children With SHANK3-related Phelan McDermid Syndrome (PMS)
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Phelan-McDermid syndrome, presbycusis