KRABD2

Summary

KRABD2 (KRAB domain containing 2, HGNC:26989) is a protein-coding gene on chromosome 17p13.1, encoding KRAB domain-containing protein 2 (Q6ZNG9).

Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration and regulation of DNA-templated transcription.

Source: NCBI Gene 124751 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_001304947

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26989
Approved symbol	KRABD2
Name	KRAB domain containing 2
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184619
Ensembl biotype	protein_coding
OMIM	620920
Entrez	124751

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 14 protein_coding

ENST00000396267, ENST00000643221, ENST00000647210, ENST00000649935, ENST00000851333, ENST00000851334, ENST00000952554, ENST00000952555, ENST00000952556, ENST00000952557, ENST00000952558, ENST00000952559, ENST00000952560, ENST00000952561

RefSeq mRNA: 2 — MANE Select: NM_001304947 NM_001304947, NM_213597

CCDS: CCDS11141, CCDS76951

Canonical transcript exons

ENST00000396267 — 2 exons

Exon	Start	End
ENSE00001524437	8358822	8370386
ENSE00001524439	8375900	8376704

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 78.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9911 / max 73.3363, expressed in 1410 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164430	1.8328	1024
164429	1.6740	865
164428	0.4843	240

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	78.04	gold quality
cortical plate	UBERON:0005343	76.56	gold quality
heart left ventricle	UBERON:0002084	76.02	gold quality
ganglionic eminence	UBERON:0004023	75.64	gold quality
cardiac ventricle	UBERON:0002082	75.36	gold quality
right atrium auricular region	UBERON:0006631	75.17	gold quality
cardiac atrium	UBERON:0002081	74.61	gold quality
heart	UBERON:0000948	73.85	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.78	gold quality
ventricular zone	UBERON:0003053	73.71	gold quality
calcaneal tendon	UBERON:0003701	73.52	gold quality
buccal mucosa cell	CL:0002336	73.36	silver quality
hindlimb stylopod muscle	UBERON:0004252	73.28	gold quality
stromal cell of endometrium	CL:0002255	73.22	gold quality
muscle of leg	UBERON:0001383	73.22	gold quality
islet of Langerhans	UBERON:0000006	72.96	gold quality
sural nerve	UBERON:0015488	72.29	gold quality
gastrocnemius	UBERON:0001388	72.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.04	gold quality
cerebellar hemisphere	UBERON:0002245	70.76	gold quality
cerebellar cortex	UBERON:0002129	70.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	70.11	gold quality
cerebellum	UBERON:0002037	69.90	gold quality
smooth muscle tissue	UBERON:0001135	69.17	gold quality
corpus callosum	UBERON:0002336	68.63	gold quality
metanephros cortex	UBERON:0010533	68.49	gold quality
lower esophagus mucosa	UBERON:0035834	67.82	gold quality
nucleus accumbens	UBERON:0001882	67.75	gold quality
left adrenal gland	UBERON:0001234	67.60	gold quality
adrenal tissue	UBERON:0018303	67.52	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-111727	no	425.14
E-GEOD-86618	no	50.87
E-ANND-3	no	3.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting KRABD2, 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-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-6507-5P	99.36	70.46	2524
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-222-5P	98.75	69.17	1242
HSA-MIR-619-5P	98.57	64.97	1988
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-8055	97.62	66.09	1023
HSA-MIR-5002-3P	95.75	67.04	542
HSA-MIR-4330	95.44	66.39	993

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

KRAB domain-containing protein 2 — Q6ZNG9 (reviewed: Q6ZNG9)

All UniProt accessions (3): Q6ZNG9, A0A2R8Y7G8, A8MX02

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (2): NP_001291876, NP_998762 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001584	Integrase_cat-core	Domain
IPR001909	KRAB	Domain
IPR012337	RNaseH-like_sf	Homologous_superfamily
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036397	RNaseH_sf	Homologous_superfamily
IPR050951

Pfam: PF01352

UniProt features (10 total): domain 2, compositionally biased region 2, modified residue 2, chain 1, region of interest 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNG9-F1	73.94	0.39

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 115, 117

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 37 (showing top): GOBP_DNA_INTEGRATION, GOBP_DNA_METABOLIC_PROCESS, ARNT2_TARGET_GENES, CHAF1B_TARGET_GENES, KMT2D_TARGET_GENES, PPARGC1A_TARGET_GENES, SETD7_TARGET_GENES, ZBTB18_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF22_TARGET_GENES, ZNF30_TARGET_GENES, ZNF577_TARGET_GENES, ZSCAN21_TARGET_GENES, MIR30D_3P, MIR30E_3P

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), DNA integration (GO:0015074)

GO Molecular Function (2): nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
DNA metabolic process	1

Protein interactions and networks

STRING

382 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRABD2	GIN1	Q9NXP7	664
KRABD2	NYNRIN	Q9P2P1	626
KRABD2	ZCCHC18	P0CG32	626
KRABD2	ZCCHC12	Q6PEW1	528
KRABD2	FAM86B1	Q8N7N1	507
KRABD2	MAP3K19	Q56UN5	492
KRABD2	DIRC1	Q969H9	479
KRABD2	CCDC9B	Q6ZUT6	447
KRABD2	A0A087WVV2	A0A087WVV2	435
KRABD2	ZNF665	Q9H7R5	431
KRABD2	KRABD3	A5PL33	407
KRABD2	TMEM54	Q969K7	393
KRABD2	RSKR	Q96LW2	386
KRABD2	SLC60A1	Q8N468	380
KRABD2	CCDC28A	Q8IWP9	380

IntAct

8 interactions, top by confidence:

A	B	Type	Score
KRBA2	HDAC7	psi-mi:“MI:0915”(physical association)	0.560
KRBA2	SCAND3	psi-mi:“MI:0915”(physical association)	0.400
BCAR1	PSMD11	psi-mi:“MI:0914”(association)	0.350
BCAR1	MYO1C	psi-mi:“MI:0914”(association)	0.350
HDAC7	KRBA2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): KRBA2 (Affinity Capture-MS), KRBA2 (Affinity Capture-MS), KRBA2 (Affinity Capture-MS), KRBA2 (Affinity Capture-MS), KRBA2 (Affinity Capture-MS), KRBA2 (Affinity Capture-MS), KRBA2 (Affinity Capture-MS), KRBA2 (Two-hybrid), KRBA2 (Affinity Capture-MS), ZBED9 (Affinity Capture-MS), KRBA2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A5Q0QMX6, A4FUB7, C0H3V9, F4HT77, F4IXT6, N4WW42, O05023, P03010, P04146, P04586, P05400, P08770, P0CF86, P0CF87, P10978, P14352, P18380, P22281, P26947, P34457, P37133, P49261, P50581, P63132, P86265, P86700, P92512, P92516, P92520, P92523, P93281, P93290, P93293, Q04977, Q0DWQ7, Q14T82, Q3EC60, Q4R6I1, Q5RBK0, Q66H30

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F4, A2T7L7, A2T812, A4Z943, A4Z944, A4Z945, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, O95789, P0CF97, P10073, P17022, P17028, P17029, P17040, P28698

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	50
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

686 predictions. Top by Δscore:

Variant	Effect	Δscore
17:8370382:GGATC:G	acceptor_gain	1.0000
17:8370383:GATC:G	acceptor_gain	1.0000
17:8370384:ATC:A	acceptor_gain	1.0000
17:8370385:TC:T	acceptor_gain	1.0000
17:8370386:CC:C	acceptor_gain	1.0000
17:8370387:C:CC	acceptor_gain	1.0000
17:8370387:C:T	acceptor_gain	1.0000
17:8371303:CCTTA:C	donor_loss	1.0000
17:8371304:CTTA:C	donor_loss	1.0000
17:8371305:TTACC:T	donor_loss	1.0000
17:8371306:TAC:T	donor_loss	1.0000
17:8371307:A:AC	donor_gain	1.0000
17:8371307:A:AT	donor_loss	1.0000
17:8371307:AC:A	donor_gain	1.0000
17:8371308:C:CA	donor_loss	1.0000
17:8371308:C:CC	donor_gain	1.0000
17:8371308:CC:C	donor_gain	1.0000
17:8371495:C:CC	acceptor_gain	1.0000
17:8370383:GATCC:G	acceptor_gain	0.9900
17:8370384:ATCCT:A	acceptor_gain	0.9900
17:8370385:TCCT:T	acceptor_gain	0.9900
17:8370386:CCT:C	acceptor_gain	0.9900
17:8370387:C:A	acceptor_gain	0.9900
17:8370387:CTAAG:C	acceptor_gain	0.9900
17:8370388:T:A	acceptor_gain	0.9900
17:8371302:CCCTT:C	donor_loss	0.9900
17:8371303:CCTT:C	donor_loss	0.9900
17:8371306:TA:T	donor_loss	0.9900
17:8371307:A:AG	donor_loss	0.9900
17:8371331:A:C	donor_gain	0.9900

AlphaMissense

2738 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:8369945:A:T	V223D	0.996
17:8369947:A:C	N222K	0.996
17:8369947:A:T	N222K	0.996
17:8370143:C:G	R157P	0.996
17:8370180:C:G	A145P	0.996
17:8370188:A:T	V142D	0.995
17:8370144:G:T	R157S	0.994
17:8370210:A:C	Y135D	0.994
17:8370095:A:G	L173P	0.993
17:8370095:A:T	L173Q	0.993
17:8370140:C:G	R158P	0.993
17:8370210:A:G	Y135H	0.991
17:8370277:A:C	F112L	0.991
17:8370277:A:T	F112L	0.991
17:8370279:A:G	F112L	0.991
17:8370031:A:C	F194L	0.989
17:8370031:A:T	F194L	0.989
17:8370033:A:G	F194L	0.989
17:8370209:T:G	Y135S	0.988
17:8370141:G:T	R158S	0.987
17:8370245:T:A	K123I	0.987
17:8370278:A:G	F112S	0.987
17:8370128:T:G	Y162S	0.986
17:8370129:A:C	Y162D	0.986
17:8369922:A:C	Y231D	0.985
17:8370023:A:G	L197P	0.985
17:8370224:A:G	F130S	0.985
17:8370244:T:A	K123N	0.985
17:8370244:T:G	K123N	0.985
17:8370023:A:T	L197H	0.984

dbSNP variants (sampled 300 via entrez): RS1000008234 (17:8366427 G>T), RS1000014266 (17:8373534 C>G,T), RS1000139054 (17:8373081 T>A,C), RS1000225855 (17:8369694 T>C,G), RS1000341371 (17:8377729 A>G,T), RS1000526466 (17:8366137 A>T), RS1000560092 (17:8368409 T>C), RS1000625030 (17:8375396 C>G), RS1000691862 (17:8376675 T>C), RS1000722703 (17:8360797 A>G), RS1000780309 (17:8368706 G>A), RS1000860551 (17:8377945 A>G), RS1000949189 (17:8360809 C>G), RS1001060407 (17:8360357 G>A), RS1001251984 (17:8374196 T>A,C)

Disease associations

OMIM: gene MIM:620920 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation	2
GSK-J4	decreases expression	1
arsenite	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, decreases reaction	1
abrine	decreases expression	1
licochalcone B	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, affects expression	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	increases expression	1
Estradiol	decreases expression	1
Formaldehyde	decreases expression	1
Lipopolysaccharides	decreases expression, decreases reaction	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Aflatoxin B1	increases methylation	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A3S9	SEES3-1V human KRBA2, clone1	Embryonic stem cell	Male
CVCL_A3T0	SEES3-1V human KRBA2, clone2	Embryonic stem cell	Male
CVCL_A3T1	SEES3-1V human KRBA2, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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