NKAPD1

Summary

NKAPD1 (NKAP domain containing 1, HGNC:25569) is a protein-coding gene on chromosome 11q23.1, encoding Uncharacterized protein NKAPD1 (Q6ZUT1). It is a selective cancer dependency (DepMap: 29.4% of cell lines).

Enables identical protein binding activity.

Source: NCBI Gene 55216 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 13 total
• Cancer dependency (DepMap): dependent in 29.4% of screened cell lines
• MANE Select transcript: NM_018195

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25569
Approved symbol	NKAPD1
Name	NKAP domain containing 1
Location	11q23.1
Locus type	gene with protein product
Status	Approved
Aliases	Ahed, FLJ10726
Ensembl gene	ENSG00000150776
Ensembl biotype	protein_coding
Entrez	55216

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000280352, ENST00000393047, ENST00000420986, ENST00000524989, ENST00000525785, ENST00000526879, ENST00000530104, ENST00000531378, ENST00000532163, ENST00000862992, ENST00000968797

RefSeq mRNA: 6 — MANE Select: NM_018195 NM_001082969, NM_001082970, NM_001301017, NM_001301019, NM_001301021, NM_018195

CCDS: CCDS41715, CCDS73383, CCDS8356

Canonical transcript exons

ENST00000393047 — 6 exons

Exon	Start	End
ENSE00001823672	112074299	112074916
ENSE00001861247	112082465	112085150
ENSE00003604421	112080409	112080558
ENSE00003647547	112081982	112082035
ENSE00003724185	112075567	112075643
ENSE00003750702	112078215	112078315

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 95.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.4321 / max 430.6084, expressed in 1808 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116699	22.4098	1808
116700	1.0223	559

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	95.33	gold quality
buccal mucosa cell	CL:0002336	94.52	gold quality
cortical plate	UBERON:0005343	93.85	gold quality
sural nerve	UBERON:0015488	91.58	gold quality
ganglionic eminence	UBERON:0004023	89.52	gold quality
monocyte	CL:0000576	89.10	gold quality
mononuclear cell	CL:0000842	88.99	gold quality
endothelial cell	CL:0000115	88.88	gold quality
leukocyte	CL:0000738	88.79	gold quality
secondary oocyte	CL:0000655	88.52	gold quality
colonic epithelium	UBERON:0000397	88.10	gold quality
adrenal tissue	UBERON:0018303	87.25	gold quality
cerebellar hemisphere	UBERON:0002245	86.87	gold quality
cerebellar cortex	UBERON:0002129	86.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.79	gold quality
muscle of leg	UBERON:0001383	86.39	gold quality
gastrocnemius	UBERON:0001388	86.30	gold quality
islet of Langerhans	UBERON:0000006	86.20	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.03	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.96	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.84	gold quality
tendon	UBERON:0000043	85.75	gold quality
endometrium	UBERON:0001295	85.59	gold quality
anterior cingulate cortex	UBERON:0009835	85.59	gold quality
cerebellum	UBERON:0002037	85.48	gold quality
cingulate cortex	UBERON:0003027	85.46	gold quality
ventricular zone	UBERON:0003053	85.25	gold quality
prefrontal cortex	UBERON:0000451	85.22	gold quality
body of pancreas	UBERON:0001150	85.22	gold quality
rectum	UBERON:0001052	85.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

110 targeting NKAPD1, 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-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-7-1-3P	99.91	71.53	4384

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 29.4% of screened cell lines.

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Nkapd1	ENSMUSG00000059820
rattus_norvegicus	Nkapd1	ENSRNOG00000009958

Protein

Protein identifiers

Uncharacterized protein NKAPD1 — Q6ZUT1 (reviewed: Q6ZUT1)

Alternative names: NKAP domain containing protein 1

All UniProt accessions (5): Q6ZUT1, E9PKA8, E9PPH9, E9PQL5, E9PSC8

Isoforms (3)

UniProt ID	Names	Canonical?
Q6ZUT1-1	1	yes
Q6ZUT1-2	2
Q6ZUT1-3	3

RefSeq proteins (6): NP_001076438, NP_001076439, NP_001287946, NP_001287948, NP_001287950, NP_060665* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR043407	Nkap_D1	Family

Pfam: PF15692

UniProt features (22 total): modified residue 6, compositionally biased region 6, sequence conflict 3, region of interest 2, cross-link 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUT1-F1	62.48	0.10

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 (8): 76, 123, 125, 126, 94, 96, 97, 8

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 157 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, AAGCAAT_MIR137, ACTACCT_MIR196A_MIR196B, CACCAGC_MIR138, TGACATY_UNKNOWN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, RYTTCCTG_ETS2_B, CETS1P54_01, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, WGGAATGY_TEF1_Q6, SCGGAAGY_ELK1_02, NUYTTEN_NIPP1_TARGETS_DN, WANG_TUMOR_INVASIVENESS_UP, COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP, ATACTGT_MIR144

GO Biological Process (0):

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
binding	1

Protein interactions and networks

STRING

348 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NKAPD1	PIH1D2	Q8WWB5	572
NKAPD1	TIMM8B	Q9Y5J9	570
NKAPD1	ZCCHC2	Q9C0B9	482
NKAPD1	RIMOC1	A6NDU8	471
NKAPD1	SPCS3	P12280	434
NKAPD1	USP38	Q8NB14	427
NKAPD1	SANBR	Q6NSI8	418
NKAPD1	C1orf21	Q9H246	413
NKAPD1	PHACTR2	O75167	410
NKAPD1	TTC27	Q6P3X3	397
NKAPD1	INTS13	Q9NVM9	368
NKAPD1	CEP20	Q96NB1	358
NKAPD1	UBE4A	Q14139	353
NKAPD1	AK9	Q5TCS8	351
NKAPD1	USP47	Q96K76	349

IntAct

232 interactions, top by confidence:

A	B	Type	Score
NKAPD1	ZNF317	psi-mi:“MI:0915”(physical association)	0.780
ZNF317	NKAPD1	psi-mi:“MI:0915”(physical association)	0.780
NKAPD1	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
SDCBP	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
RBM39	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
NKAPD1	BEND7	psi-mi:“MI:0915”(physical association)	0.720
NKAPD1	CEP70	psi-mi:“MI:0915”(physical association)	0.720
STAC3	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
SDCBP2	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
THAP1	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
NKAPD1	RBM39	psi-mi:“MI:0915”(physical association)	0.720
CEP70	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
NKAPD1	STAC3	psi-mi:“MI:0915”(physical association)	0.720
NKAPD1	SDCBP2	psi-mi:“MI:0915”(physical association)	0.720
BEND7	NKAPD1	psi-mi:“MI:0915”(physical association)	0.720
NKAPD1	THAP1	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (246): C11orf57 (Two-hybrid), C11orf57 (Two-hybrid), C11orf57 (Two-hybrid), C11orf57 (Two-hybrid), C11orf57 (Two-hybrid), ZNF317 (Two-hybrid), SNRNP25 (Two-hybrid), CEP70 (Two-hybrid), BEND7 (Two-hybrid), STAC3 (Two-hybrid), C11orf57 (Affinity Capture-MS), C11orf57 (Affinity Capture-MS), SRRM2 (Affinity Capture-MS), PNN (Affinity Capture-MS), CSNK2A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1S3XQD6, A0A1S4AX27, A1A5I1, A2AR02, A6QLS2, B0BN49, G2TRQ9, O14256, O55035, P30189, P30414, P41512, Q04750, Q07050, Q13427, Q27450, Q28EE8, Q3KPW4, Q4V9W2, Q505I5, Q59LQ5, Q5BKY9, Q5R8J6, Q5RJP9, Q5VTL8, Q5XHJ5, Q5ZLM8, Q6AXY7, Q6BNE1, Q6NQD9, Q6NWI1, Q6ZUT1, Q751P0, Q7L4I2, Q7YR26, Q80SY5, Q8GWY0, Q8N9E0, Q8N9Q2, Q8R0F5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 72 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
RNA splicing	8	11.6×	2e-04
mRNA processing	8	10.3×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

852 predictions. Top by Δscore:

Variant	Effect	Δscore
11:112075561:TTTCA:T	acceptor_loss	1.0000
11:112075562:TTCAG:T	acceptor_loss	1.0000
11:112075563:TCA:T	acceptor_loss	1.0000
11:112075564:CAGA:C	acceptor_loss	1.0000
11:112075565:A:AG	acceptor_gain	1.0000
11:112075565:AG:A	acceptor_loss	1.0000
11:112075566:G:GA	acceptor_gain	1.0000
11:112075566:GATT:G	acceptor_gain	1.0000
11:112075773:G:GG	donor_gain	1.0000
11:112078204:A:AG	acceptor_gain	1.0000
11:112078205:A:G	acceptor_gain	1.0000
11:112078207:A:AG	acceptor_gain	1.0000
11:112078212:TA:T	acceptor_loss	1.0000
11:112078213:A:AG	acceptor_gain	1.0000
11:112078213:A:T	acceptor_loss	1.0000
11:112078214:G:GG	acceptor_gain	1.0000
11:112078292:G:GT	donor_gain	1.0000
11:112078318:G:GT	donor_gain	1.0000
11:112080404:TTTA:T	acceptor_loss	1.0000
11:112080405:TTA:T	acceptor_loss	1.0000
11:112080406:TAG:T	acceptor_loss	1.0000
11:112080407:A:AG	acceptor_gain	1.0000
11:112080407:AGCC:A	acceptor_gain	1.0000
11:112080407:AGCCG:A	acceptor_gain	1.0000
11:112080408:G:GA	acceptor_gain	1.0000
11:112080408:GC:G	acceptor_gain	1.0000
11:112080408:GCC:G	acceptor_gain	1.0000
11:112080408:GCCG:G	acceptor_gain	1.0000
11:112080408:GCCGG:G	acceptor_gain	1.0000
11:112080488:G:GT	donor_gain	1.0000

AlphaMissense

1971 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:112081983:T:A	W108R	0.999
11:112081983:T:C	W108R	0.999
11:112081985:G:C	W108C	0.999
11:112081985:G:T	W108C	0.999
11:112075606:T:C	L11P	0.998
11:112078236:T:A	W31R	0.998
11:112078236:T:C	W31R	0.998
11:112078238:G:C	W31C	0.998
11:112078238:G:T	W31C	0.998
11:112075618:T:A	I15N	0.997
11:112075621:G:C	R16P	0.997
11:112075643:G:C	K23N	0.997
11:112075643:G:T	K23N	0.997
11:112078237:G:C	W31S	0.997
11:112075603:T:A	L10H	0.996
11:112075606:T:A	L11Q	0.996
11:112075613:T:A	N13K	0.996
11:112075613:T:G	N13K	0.996
11:112075618:T:G	I15S	0.996
11:112075635:C:G	H21D	0.996
11:112078235:G:A	M30I	0.996
11:112078235:G:C	M30I	0.996
11:112078235:G:T	M30I	0.996
11:112082022:T:C	F121L	0.996
11:112082024:T:A	F121L	0.996
11:112082024:T:G	F121L	0.996
11:112075593:G:A	G7R	0.995
11:112075593:G:C	G7R	0.995
11:112075603:T:C	L10P	0.995
11:112075618:T:C	I15T	0.995

dbSNP variants (sampled 300 via entrez): RS1000001540 (11:112080290 A>G), RS1000003560 (11:112084206 C>G), RS1000436736 (11:112083974 C>T), RS1000856537 (11:112075312 C>T), RS1001036450 (11:112079058 T>A), RS1001046719 (11:112082182 T>C), RS1001611977 (11:112083473 G>A), RS1001738260 (11:112076617 T>A,C), RS1001770993 (11:112076272 A>C,G), RS1001883229 (11:112085144 CTT>C), RS1002020406 (11:112084889 A>C), RS1002318759 (11:112077888 C>G,T), RS1002445481 (11:112078287 A>G), RS1002696538 (11:112081290 C>T), RS1002775474 (11:112074499 C>A,G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	decreases expression	1
aflatoxin B2	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
MT19c compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Gallic Acid	increases expression	1
Hydrogen Peroxide	affects expression	1
Plant Extracts	affects cotreatment, increases expression	1
Theophylline	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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