PNCK

pregnancy up-regulated nonubiquitous CaM kinase, the group of Calmodulin dependent protein kinases

Basic information

Region (hg38): X:153669733-153689010

Links

ENSG00000130822 ∙ NCBI:139728 ∙ OMIM:300680 ∙ HGNC:13415 ∙ Uniprot:Q6P2M8 ∙ 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 PNCK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNCK 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				1	1	2
missense			6	4		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1	1
Total	0	0	6	5	2

Variants in PNCK

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

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

Position	Type	Phenotype	Significance	ClinVar
X-153670487-G-A			Likely benign (Feb 01, 2023)
X-153670532-G-A			Benign (Feb 22, 2018)
X-153670772-C-T		not specified	Likely benign (Jul 12, 2022)
X-153670773-G-A		not specified	Uncertain significance (Jan 23, 2023)
X-153670927-C-T		not specified	Likely benign (Feb 28, 2024)
X-153671092-T-C		not specified	Uncertain significance (Nov 27, 2023)
X-153671301-C-T		not specified	Uncertain significance (Oct 02, 2023)
X-153671318-T-G		not specified	Uncertain significance (Nov 08, 2022)
X-153671960-C-T		not specified	Uncertain significance (Mar 06, 2023)
X-153672060-G-A		PNCK-related condition	Likely benign (Sep 09, 2024)
X-153672172-C-T		not specified	Conflicting classifications of pathogenicity (May 26, 2024)
X-153672651-G-A		not specified	Uncertain significance (Oct 10, 2023)
X-153672654-C-A		not specified	Likely benign (Nov 12, 2021)
X-153672995-G-A			Benign (Dec 01, 2019)
X-153673078-T-C		not specified	Uncertain significance (Nov 07, 2022)
X-153674082-A-G		not specified	Uncertain significance (Jul 09, 2021)
X-153674138-C-T		not specified	Uncertain significance (Sep 27, 2021)
X-153688564-C-T		not specified	Likely benign (Jul 01, 2016)
X-153688569-G-T			Uncertain significance (Jan 12, 2022)
X-153688569-GA-G		not specified	Likely benign (Dec 28, 2017)
X-153688570-A-G		not specified • Creatine transporter deficiency • Creatine deficiency syndrome 1 • Inborn genetic diseases • SLC6A8-related disorder	Benign (Jul 15, 2024)
X-153688575-A-G		Creatine transporter deficiency	Uncertain significance (Mar 23, 2023)
X-153688579-CGAA-C		Creatine transporter deficiency	Uncertain significance (Sep 01, 2022)
X-153688580-G-A		Creatine transporter deficiency	Likely benign (Jun 09, 2023)
X-153688581-A-G			Uncertain significance (Jul 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNCK	protein_coding	protein_coding	ENST00000447676	11	19281

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000102	0.808	125722	13	3	125738	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	132	191	0.693	0.0000168	2746
Missense in Polyphen		45	67.752	0.66419		939
Synonymous	-0.0343	84	83.6	1.00	0.00000761	862
Loss of Function	1.29	10	15.5	0.646	0.00000117	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.0000980
Ashkenazi Jewish	0.00	0.00
East Asian	0.000145	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000751	0.0000527
Middle Eastern	0.000145	0.000109
South Asian	0.000322	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium/calmodulin-dependent protein kinase belonging to a proposed calcium-triggered signaling cascade. In vitro phosphorylates CREB1 and SYN1/synapsin I. Phosphorylates and activates CAMK1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.674
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.409
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.690

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnck

Gene ontology

• Biological process: protein phosphorylation
• Cellular component: nucleus;cytoplasm
• Molecular function: calmodulin-dependent protein kinase activity;calmodulin binding;ATP binding