NKPD1

Summary

NKPD1 (NTPase KAP family P-loop domain containing 1, HGNC:24739) is a protein-coding gene on chromosome 19q13.32, encoding NTPase KAP family P-loop domain-containing protein 1 (Q17RQ9).

Predicted to be located in membrane.

Source: NCBI Gene 284353 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 156 total
• MANE Select transcript: NM_198478

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24739
Approved symbol	NKPD1
Name	NTPase KAP family P-loop domain containing 1
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33600
Ensembl gene	ENSG00000179846
Ensembl biotype	protein_coding
Entrez	284353

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000317951, ENST00000589776, ENST00000686631

RefSeq mRNA: 1 — MANE Select: NM_198478 NM_198478

Canonical transcript exons

ENST00000686631 — 5 exons

Exon	Start	End
ENSE00002041647	45158663	45159100
ENSE00003546915	45155785	45155916
ENSE00003903316	45160060	45160221
ENSE00003927709	45160925	45160982
ENSE00003930258	45149744	45153775

Expression profiles

Bgee: expression breadth broad, 87 present calls, max score 80.34.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	80.34	gold quality
skin of leg	UBERON:0001511	78.72	gold quality
zone of skin	UBERON:0000014	77.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.55	silver quality
upper leg skin	UBERON:0004262	68.44	gold quality
tendon of biceps brachii	UBERON:0008188	65.74	gold quality
skin of hip	UBERON:0001554	64.89	gold quality
lower esophagus mucosa	UBERON:0035834	63.00	gold quality
bone marrow cell	CL:0002092	58.63	gold quality
vagina	UBERON:0000996	57.96	gold quality
sural nerve	UBERON:0015488	56.56	gold quality
right uterine tube	UBERON:0001302	55.79	gold quality
cortical plate	UBERON:0005343	54.96	silver quality
prefrontal cortex	UBERON:0000451	54.95	gold quality
esophagus mucosa	UBERON:0002469	54.81	gold quality
penis	UBERON:0000989	54.18	silver quality
parotid gland	UBERON:0001831	53.74	gold quality
oviduct epithelium	UBERON:0004804	53.62	gold quality
medial globus pallidus	UBERON:0002477	50.83	gold quality
cerebellar cortex	UBERON:0002129	49.98	silver quality
cerebellar hemisphere	UBERON:0002245	49.95	silver quality
right hemisphere of cerebellum	UBERON:0014890	49.89	gold quality
ectocervix	UBERON:0012249	49.86	gold quality
frontal cortex	UBERON:0001870	49.57	gold quality
nipple	UBERON:0002030	49.47	gold quality
gingiva	UBERON:0001828	49.39	gold quality
cerebellum	UBERON:0002037	49.39	silver quality
stromal cell of endometrium	CL:0002255	49.08	gold quality
gingival epithelium	UBERON:0001949	48.91	gold quality
prostate gland	UBERON:0002367	48.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting NKPD1, 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-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-3064-5P	99.26	66.13	1497
HSA-MIR-3085-3P	99.26	66.16	1490
HSA-MIR-6504-5P	99.26	65.95	1487
HSA-MIR-5190	99.15	67.76	1234
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-412-3P	98.86	66.89	712
HSA-MIR-6754-3P	98.84	66.60	889
HSA-MIR-6885-5P	98.71	64.33	902

Literature-anchored findings (GeneRIF, showing 2)

• altered membrane NTPase activity is a biochemical hallmark of HPRT deficiency, but species and cell-type differences have to be considered (PMID:15935074)
• Study suggests that nonsynonymous variation in the gene NKPD1 affects depressive symptoms in the general population. (PMID:27745872)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nkpd1	ENSDARG00000075698
mus_musculus	Nkpd1	ENSMUSG00000060621
rattus_norvegicus	Nkpd1	ENSRNOG00000043378

Protein

Protein identifiers

NTPase KAP family P-loop domain-containing protein 1 — Q17RQ9 (reviewed: Q17RQ9)

All UniProt accessions (2): A0A7N4I390, Q17RQ9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_940880* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011646	KAP_P-loop	Domain
IPR052754	NTPase_KAP_P-loop	Family

Pfam: PF07693

UniProt features (10 total): transmembrane region 3, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q17RQ9-F1	71.68	0.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): BENPORATH_ES_WITH_H3K27ME3, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, CP2_01, HSF1_01, NFE2L2.V2, HMG20B_TARGET_GENES, NCOA2_TARGET_GENES, ZNF436_TARGET_GENES, MIR6764_5P, MIR5701, MIR6754_3P, GSE14350_IL2RB_KO_VS_WT_TEFF_DN, GSE15767_MED_VS_SCS_MAC_LN_UP, GSE12003_4D_VS_8D_CULTURE_MIR223_KO_BM_PROGENITOR_UP, HDGF_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

710 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NKPD1	ZNF34	Q8IZ26	584
NKPD1	DTWD1	Q8N5C7	448
NKPD1	HYCC2	Q8IXS8	428
NKPD1	PTH2R	P49190	401
NKPD1	GEMIN7	Q9H840	397
NKPD1	DNAJC5G	Q8N7S2	394
NKPD1	TRAPPC6A	O75865	392
NKPD1	RABL2A	Q9UBK7	388
NKPD1	CXXC5	Q7LFL8	382
NKPD1	MRGPRF	Q96AM1	380
NKPD1	CLASRP	Q8N2M8	379
NKPD1	SUSD5	O60279	362
NKPD1	CLPTM1	O96005	359
NKPD1	BCL11B	Q9C0K0	341
NKPD1	TRIM54	Q9BYV2	336

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GU71, A6QPI4, B2RV13, D4A6L0, E1BBQ2, F1LQY6, G3UW36, O08856, P15382, P53801, P55199, P56182, Q08CB3, Q0VF94, Q148E1, Q17RQ9, Q2KJ58, Q32Q90, Q4R5F9, Q4V8A6, Q4VA36, Q5I0I4, Q5NVI6, Q5R8Q2, Q5T6X4, Q5T848, Q5XII8, Q68EN5, Q6P767, Q8C419, Q8CHT6, Q8R143, Q8R1T1, Q8TBN0, Q8VDV3, Q8WUX9, Q90YH8, Q91WM6, Q91ZP9, Q96IL0

Diamond homologs: Q0VF94, Q17RQ9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	142
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

641 predictions. Top by Δscore:

Variant	Effect	Δscore
19:45155780:CTCA:C	donor_loss	1.0000
19:45155781:TCA:T	donor_loss	1.0000
19:45155782:CA:C	donor_loss	1.0000
19:45155783:A:AC	donor_gain	1.0000
19:45155783:AC:A	donor_gain	1.0000
19:45155784:C:CC	donor_gain	1.0000
19:45155784:CC:C	donor_gain	1.0000
19:45155912:GATGT:G	acceptor_gain	1.0000
19:45155913:ATGT:A	acceptor_gain	1.0000
19:45155914:TGT:T	acceptor_gain	1.0000
19:45155914:TGTC:T	acceptor_loss	1.0000
19:45155915:GT:G	acceptor_gain	1.0000
19:45155915:GTC:G	acceptor_loss	1.0000
19:45155916:TC:T	acceptor_loss	1.0000
19:45155917:C:CA	acceptor_loss	1.0000
19:45155917:C:CC	acceptor_gain	1.0000
19:45155918:T:C	acceptor_loss	1.0000
19:45155920:G:GC	acceptor_gain	1.0000
19:45155924:T:C	acceptor_gain	1.0000
19:45155924:T:TC	acceptor_gain	1.0000
19:45155920:G:C	acceptor_gain	0.9900
19:45155923:G:GC	acceptor_gain	0.9900
19:45153776:C:CC	acceptor_gain	0.9800
19:45155923:G:C	acceptor_gain	0.9800
19:45156635:AGGGC:A	donor_gain	0.9800
19:45160054:CCGTA:C	donor_loss	0.9800
19:45160055:CGTA:C	donor_loss	0.9800
19:45160056:GTAC:G	donor_loss	0.9800
19:45160057:TA:T	donor_loss	0.9800
19:45160059:C:G	donor_loss	0.9800

AlphaMissense

5368 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:45152450:A:G	W441R	0.999
19:45152450:A:T	W441R	0.999
19:45152869:A:T	V301D	0.999
19:45153560:A:G	W71R	0.999
19:45153560:A:T	W71R	0.999
19:45153594:A:C	F59L	0.999
19:45153594:A:T	F59L	0.999
19:45153596:A:G	F59L	0.999
19:45152471:A:G	W434R	0.998
19:45152471:A:T	W434R	0.998
19:45153014:C:G	A253P	0.998
19:45153558:C:A	W71C	0.998
19:45153558:C:G	W71C	0.998
19:45152202:G:C	N523K	0.997
19:45152202:G:T	N523K	0.997
19:45152432:A:G	W447R	0.997
19:45152432:A:T	W447R	0.997
19:45152433:G:C	S446R	0.997
19:45152433:G:T	S446R	0.997
19:45152435:T:G	S446R	0.997
19:45152448:C:A	W441C	0.997
19:45152448:C:G	W441C	0.997
19:45152863:A:G	L303P	0.997
19:45153159:G:C	F204L	0.997
19:45153159:G:T	F204L	0.997
19:45153160:A:G	F204S	0.997
19:45153161:A:G	F204L	0.997
19:45152560:A:T	V404D	0.996
19:45152857:A:G	F305S	0.996
19:45152875:C:G	R299P	0.996

dbSNP variants (sampled 300 via entrez): RS1000155211 (19:45155371 G>A), RS1000200920 (19:45152931 T>C), RS1000505161 (19:45157519 C>G), RS1000537655 (19:45157793 C>T), RS1000690759 (19:45161107 T>A), RS1000783180 (19:45162439 C>A), RS1001213936 (19:45162589 C>G), RS1001261069 (19:45158925 C>T), RS1001284484 (19:45164735 G>A,T), RS1001634860 (19:45153923 A>G), RS1001687505 (19:45157201 A>T), RS1001925191 (19:45162153 C>G,T), RS1001958550 (19:45149485 A>G,T), RS1002092754 (19:45149252 C>T), RS1002265350 (19:45160198 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

6 associations (top):

Study	Trait	p-value
GCST004069_16	Cerebrospinal fluid AB1-42 levels	6.000000e-10
GCST007320_16	Alzheimer’s disease or family history of Alzheimer’s disease	2.000000e-38
GCST007320_87	Alzheimer’s disease or family history of Alzheimer’s disease	7.000000e-09
GCST007827_13	Alzheimer’s disease or HDL levels (pleiotropy)	7.000000e-22
GCST007827_3	Alzheimer’s disease or HDL levels (pleiotropy)	1.000000e-97
GCST007827_8	Alzheimer’s disease or HDL levels (pleiotropy)	3.000000e-36

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004670	beta-amyloid 1-42 measurement
EFO:0009268	family history of Alzheimer’s disease
EFO:0004612	high density lipoprotein cholesterol measurement

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
Benzo(a)pyrene	affects methylation, decreases expression	2
aristolochic acid I	decreases expression	1
methyleugenol	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
avobenzone	decreases expression	1
abrine	increases expression	1
Cisplatin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Valproic Acid	increases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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