KRABD1

Summary

KRABD1 (KRAB domain containing 1, HGNC:38708) is a protein-coding gene on chromosome 3p22.1, encoding KRAB domain-containing protein 1 (C9JBD0).

Predicted to be involved in regulation of DNA-templated transcription.

Source: NCBI Gene 100506243 — RefSeq curated summary.

At a glance

• GWAS associations: 14
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001205272

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:38708
Approved symbol	KRABD1
Name	KRAB domain containing 1
Location	3p22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000240747
Ensembl biotype	protein_coding
Entrez	100506243

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000383748, ENST00000418176, ENST00000463888

RefSeq mRNA: 1 — MANE Select: NM_001205272 NM_001205272

CCDS: CCDS54572

Canonical transcript exons

ENST00000383748 — 5 exons

Exon	Start	End
ENSE00001556263	42936386	42936455
ENSE00003705571	42941958	42942071
ENSE00003706390	42938850	42938931
ENSE00003710607	42941226	42941352
ENSE00003901243	42942538	42942792

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 99.17.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5950 / max 163.7463, expressed in 42 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36297	2.8995	763
36284	0.5950	42

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	99.17	gold quality
left testis	UBERON:0004533	99.15	gold quality
testis	UBERON:0000473	98.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.71	gold quality
stromal cell of endometrium	CL:0002255	87.73	gold quality
ventricular zone	UBERON:0003053	86.77	gold quality
ganglionic eminence	UBERON:0004023	84.30	gold quality
islet of Langerhans	UBERON:0000006	81.93	gold quality
left ovary	UBERON:0002119	80.75	gold quality
mucosa of stomach	UBERON:0001199	79.92	gold quality
ovary	UBERON:0000992	79.11	gold quality
right ovary	UBERON:0002118	78.62	gold quality
left uterine tube	UBERON:0001303	78.53	gold quality
calcaneal tendon	UBERON:0003701	78.45	gold quality
cortical plate	UBERON:0005343	78.26	gold quality
adenohypophysis	UBERON:0002196	78.21	gold quality
tibial artery	UBERON:0007610	77.88	gold quality
popliteal artery	UBERON:0002250	77.86	gold quality
left lobe of thyroid gland	UBERON:0001120	77.74	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.41	gold quality
thyroid gland	UBERON:0002046	77.36	gold quality
endometrium	UBERON:0001295	77.29	gold quality
right adrenal gland cortex	UBERON:0035827	77.21	gold quality
right coronary artery	UBERON:0001625	77.12	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	77.11	gold quality
right adrenal gland	UBERON:0001233	77.10	gold quality
lower esophagus	UBERON:0013473	76.85	gold quality
lower esophagus muscularis layer	UBERON:0035833	76.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.76	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	27.40
E-CURD-11	no	52.10
E-ANND-3	no	2.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting KRABD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-499A-3P	99.18	69.20	1392
HSA-MIR-499B-3P	99.18	69.27	1391
HSA-MIR-890	97.47	68.67	982
HSA-MIR-582-3P	96.69	67.38	1019
HSA-MIR-4774-5P	95.92	68.27	827

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-89o9.6	ENSDARG00000075639
mus_musculus	Zfp65	ENSMUSG00000071281
drosophila_melanogaster	CG9609	FBGN0030787
caenorhabditis_elegans		WBGENE00009866
caenorhabditis_elegans	M04C9.4	WBGENE00010859
caenorhabditis_elegans		WBGENE00011710
caenorhabditis_elegans		WBGENE00012969
caenorhabditis_elegans	F57C9.4	WBGENE00019011
caenorhabditis_elegans		WBGENE00019589
caenorhabditis_elegans		WBGENE00022016
caenorhabditis_elegans		WBGENE00271744

Paralogs (2): ZNF200 (ENSG00000010539), ZNF532 (ENSG00000074657)

Protein

Protein identifiers

KRAB domain-containing protein 1 — C9JBD0 (reviewed: C9JBD0)

All UniProt accessions (1): C9JBD0

Isoforms (2)

UniProt ID	Names	Canonical?
C9JBD0-1	1	yes
C9JBD0-2	2

RefSeq proteins (1): NP_001192201* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR050169	Krueppel_C2H2_ZnF	Family

Pfam: PF01352

UniProt features (3 total): chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JBD0-F1	66.75	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, chr3p22, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP, FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ID1_TARGET_GENES, MIR4698, MIR493_5P, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN, MIR511_3P

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1

Protein interactions and networks

STRING

94 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRABD1	KRTAP19-4	Q3LI73	692
KRABD1	RFLNB	Q8N5W9	418
KRABD1	PALS2	Q9NZW5	401
KRABD1	PPP1R18	Q6NYC8	397
KRABD1	PTGR2	Q8N8N7	373
KRABD1	TMT1B	Q6UX53	351
KRABD1	LCE3D	Q9BYE3	348
KRABD1	B3GALT4	O96024	348
KRABD1	ABI3BP	Q7Z7G0	323
KRABD1	LRRC15	Q8TF66	305
KRABD1	PRUNE2	Q8WUY3	278
KRABD1	SLC39A7	Q92504	269
KRABD1	ACOX2	Q99424	248
KRABD1	ERRFI1	Q9UJM3	240
KRABD1	PALS1	Q8N3R9	228

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A023IWD9, A0A023IWE0, A0A023IWE1, A0A023IWG1, A0A023IWG2, A0A023IWI8, A0A023IWK3, A0A023IWK5, A0A023IWM4, A0A023UA23, A0A023UBA8, A0A023UBX6, A0A023UBY3, A2C4H7, A2SJD1, A2SSV2, A8W7M4, A8W7M6, A8W7M9, A8W7N1, A8W7N4, A8W7N6, A8W7P3, A9ILJ1, B1Y0M2, C3K860, C9JBD0, O29982, O83699, P08061, P08229, P0CU65, P0DKH4, P22660, P33581, P39495, P55536, P81080, P85498, Q03284

Diamond homologs: A1L1L7, A3KN32, A3KN36, A6NFI3, A6NM28, A6NN14, A6QLU5, A7MBI1, A8K8V0, A8MTY0, A8MWA4, B4DU55, C9JBD0, G3X9G7, O60765, O75290, O94892, O95780, P0C7X2, P10072, P15622, P16373, P16374, P17023, P17032, P17097, P17098, P21506, P52742, P59923, Q06730, Q08DG8, Q16587, Q29RZ4, Q2TL60, Q3V080, Q49AA0, Q4R6C2, Q4V8A8, Q5FWF6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

617 predictions. Top by Δscore:

Variant	Effect	Δscore
3:42938848:A:AG	acceptor_gain	1.0000
3:42938849:G:GG	acceptor_gain	1.0000
3:42941951:C:A	acceptor_gain	0.9900
3:42941956:A:AG	acceptor_gain	0.9900
3:42941957:G:GG	acceptor_gain	0.9900
3:42938849:GC:G	acceptor_gain	0.9800
3:42941954:GCA:G	acceptor_gain	0.9800
3:42941957:GTGC:G	acceptor_gain	0.9800
3:42941957:GTGCC:G	acceptor_gain	0.9800
3:42938844:CTTCA:C	acceptor_loss	0.9700
3:42938845:TTCA:T	acceptor_loss	0.9700
3:42938848:AGC:A	acceptor_loss	0.9700
3:42941955:CAGTG:C	acceptor_loss	0.9700
3:42941956:A:G	acceptor_loss	0.9700
3:42941956:AGT:A	acceptor_gain	0.9700
3:42941957:G:GT	acceptor_loss	0.9700
3:42941957:GT:G	acceptor_gain	0.9700
3:42941957:GTG:G	acceptor_gain	0.9700
3:42938849:GCA:G	acceptor_gain	0.9600
3:42941218:CGTT:C	acceptor_loss	0.9500
3:42941219:GTTTC:G	acceptor_loss	0.9500
3:42941222:TCA:T	acceptor_loss	0.9500
3:42941223:CAG:C	acceptor_loss	0.9500
3:42941225:G:GC	acceptor_loss	0.9500
3:42941313:G:T	donor_gain	0.9500
3:42941348:TGTAG:T	donor_loss	0.9500
3:42941350:TAG:T	donor_loss	0.9500
3:42941351:AG:A	donor_loss	0.9500
3:42941352:GG:G	donor_loss	0.9500
3:42941353:G:GT	donor_loss	0.9500

AlphaMissense

820 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:42941238:T:C	F17L	0.949
3:42941240:T:A	F17L	0.949
3:42941240:T:G	F17L	0.949
3:42941259:T:C	F24L	0.878
3:42941261:C:A	F24L	0.878
3:42941261:C:G	F24L	0.878
3:42941321:G:A	M44I	0.857
3:42941321:G:C	M44I	0.857
3:42941321:G:T	M44I	0.857
3:42941239:T:G	F17C	0.848
3:42941276:G:C	W29C	0.843
3:42941276:G:T	W29C	0.843
3:42941346:T:C	F53L	0.805
3:42941348:T:A	F53L	0.805
3:42941348:T:G	F53L	0.805
3:42941307:T:G	Y40D	0.793
3:42941330:C:A	N47K	0.791
3:42941330:C:G	N47K	0.791
3:42941260:T:C	F24S	0.786
3:42941251:C:A	A21D	0.783
3:42941250:G:C	A21P	0.772
3:42941974:A:C	K60N	0.764
3:42941974:A:T	K60N	0.764
3:42941274:T:A	W29R	0.752
3:42941274:T:C	W29R	0.752
3:42941263:C:T	T25I	0.747
3:42941300:G:C	R37S	0.736
3:42941300:G:T	R37S	0.736
3:42941239:T:C	F17S	0.729
3:42941273:A:C	E28D	0.724

dbSNP variants (sampled 300 via entrez): RS1000169940 (3:42938206 C>A), RS1001051662 (3:42935144 A>G), RS1001201465 (3:42939363 G>A), RS1001626683 (3:42937821 G>GGGA), RS1001643133 (3:42939711 T>C), RS1002729335 (3:42936748 C>G), RS1002892633 (3:42939337 A>G), RS1002912043 (3:42938205 T>C), RS1003269762 (3:42936535 G>A), RS1003406151 (3:42939491 C>G), RS1003626790 (3:42936756 C>T), RS1003751312 (3:42943061 T>C), RS1004036286 (3:42941937 T>C), RS1004101535 (3:42941406 T>C), RS1004680943 (3:42937735 G>A)

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

14 associations (top):

Study	Trait	p-value
GCST002595_14	Clozapine-induced agranulocytosis	3.000000e-06
GCST004608_69	Granulocyte percentage of myeloid white cells	5.000000e-19
GCST004609_107	Monocyte percentage of white cells	8.000000e-38
GCST004610_57	White blood cell count	2.000000e-14
GCST004613_100	Sum neutrophil eosinophil counts	2.000000e-11
GCST004614_138	Granulocyte count	4.000000e-12
GCST004620_138	Sum basophil neutrophil counts	4.000000e-11
GCST004625_65	Monocyte count	4.000000e-65
GCST004626_26	Myeloid white cell count	6.000000e-18
GCST004629_31	Neutrophil count	1.000000e-10
GCST90002381_144	Eosinophil count	6.000000e-15
GCST90002389_15	Lymphocyte percentage of white cells	1.000000e-15
GCST90002398_120	Neutrophil count	2.000000e-23
GCST90002407_45	White blood cell count	2.000000e-24

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007997	granulocyte percentage of myeloid white cells
EFO:0007989	monocyte percentage of leukocytes
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0007987	granulocyte count
EFO:0005090	basophil count
EFO:0005091	monocyte count
EFO:0007993	lymphocyte percentage of leukocytes

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.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
sodium chromate(VI)	decreases expression, decreases reaction	1
2-palmitoylglycerol	increases expression	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Benzo(a)pyrene	affects expression	1
Cadmium	increases expression, increases abundance	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Valproic Acid	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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