NKPD1

NTPase KAP family P-loop domain containing 1

Basic information

Region (hg38): 19:45149743-45160982

Links

ENSG00000179846 ∙ NCBI:284353 ∙ ∙ HGNC:24739 ∙ Uniprot:Q17RQ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NKPD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKPD1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			44	6		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	6	0

Variants in NKPD1

This is a list of pathogenic ClinVar variants found in the NKPD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-45151975-A-G		not specified	Likely benign (Jan 23, 2023)
19-45152017-T-G		not specified	Uncertain significance (Dec 20, 2021)
19-45152036-C-G		not specified	Uncertain significance (Mar 21, 2023)
19-45152053-G-C		not specified	Likely benign (Jun 09, 2022)
19-45152056-C-A		not specified	Uncertain significance (Apr 07, 2023)
19-45152062-G-A		not specified	Uncertain significance (Mar 30, 2024)
19-45152089-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-45152105-G-A		not specified	Uncertain significance (Dec 12, 2022)
19-45152161-G-T		not specified	Uncertain significance (Feb 28, 2024)
19-45152175-C-T		not specified	Uncertain significance (Dec 14, 2021)
19-45152285-G-A		not specified	Uncertain significance (Nov 03, 2023)
19-45152369-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-45152381-C-T		not specified	Uncertain significance (Feb 14, 2024)
19-45152469-C-G		not specified	Uncertain significance (May 12, 2024)
19-45152479-G-A		not specified	Uncertain significance (May 26, 2024)
19-45152523-C-G		not specified	Uncertain significance (Aug 13, 2021)
19-45152540-C-A		not specified	Uncertain significance (Mar 21, 2023)
19-45152570-G-A		not specified	Uncertain significance (Mar 08, 2024)
19-45152636-G-A		not specified	Uncertain significance (May 09, 2023)
19-45152668-T-C		not specified	Uncertain significance (May 17, 2023)
19-45152684-C-T		not specified	Uncertain significance (May 30, 2022)
19-45152734-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-45152806-G-T		not specified	Uncertain significance (Mar 13, 2023)
19-45152875-C-T		not specified	Uncertain significance (May 21, 2024)
19-45152917-T-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKPD1	protein_coding	protein_coding	ENST00000317951	4	10401

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.04e-7	0.903	123321	0	97	123418	0.000393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	341	479	0.712	0.0000306	5194
Missense in Polyphen		96	161.66	0.59384		1785
Synonymous	1.81	196	231	0.849	0.0000163	1771
Loss of Function	1.66	13	21.3	0.611	0.00000109	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00194	0.00145
Ashkenazi Jewish	0.000328	0.000301
East Asian	0.00	0.00
Finnish	0.000437	0.000374
European (Non-Finnish)	0.000617	0.000511
Middle Eastern	0.00	0.00
South Asian	0.000140	0.000131
Other	0.000573	0.000500

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.324
• ghis: 0.414

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.482

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nkpd1

Gene ontology

• Cellular component: integral component of membrane