PASK

PAS domain containing serine/threonine kinase, the group of PAS domain containing

Basic information

Region (hg38): 2:241106099-241150264

Links

ENSG00000115687 ∙ NCBI:23178 ∙ OMIM:607505 ∙ HGNC:17270 ∙ Uniprot:Q96RG2 ∙ 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 PASK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PASK 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				8	8	16
missense			117	14	8	139
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	118	22	16

Variants in PASK

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

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

Position	Type	Phenotype	Significance	ClinVar
2-241106582-C-T			Benign (Dec 31, 2019)
2-241106597-T-G		not specified	Uncertain significance (Apr 25, 2022)
2-241106611-G-A			Benign (Feb 20, 2018)
2-241106625-C-T		not specified	Uncertain significance (Aug 14, 2024)
2-241106657-G-A		not specified	Uncertain significance (Jul 22, 2024)
2-241106677-G-C		not specified	Uncertain significance (Aug 27, 2024)
2-241106677-G-T		not specified	Uncertain significance (Jun 05, 2024)
2-241106678-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-241106706-C-A		not specified	Uncertain significance (May 02, 2024)
2-241106708-G-C		not specified	Uncertain significance (Sep 26, 2024)
2-241107367-C-T		not specified	Likely benign (Dec 18, 2023)
2-241107464-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-241107467-G-T		not specified	Uncertain significance (Mar 31, 2023)
2-241108179-G-C		not specified	Uncertain significance (Oct 21, 2024)
2-241108186-C-T			Likely benign (May 29, 2018)
2-241108250-G-A		not specified	Uncertain significance (Aug 11, 2021)
2-241108271-G-A		not specified	Uncertain significance (Dec 07, 2021)
2-241108288-C-T			Likely benign (Aug 09, 2018)
2-241112239-C-T		not specified • Chronic kidney disease	Uncertain significance (Jan 01, 2019)
2-241112240-G-A		PASK-related disorder	Uncertain significance (May 22, 2023)
2-241112253-G-A		not specified	Uncertain significance (Jul 15, 2021)
2-241112261-G-A		not specified	Uncertain significance (May 18, 2022)
2-241112327-G-A		not specified	Uncertain significance (May 23, 2023)
2-241112414-C-T		PASK-related disorder	Likely benign (Apr 24, 2018)
2-241112415-G-A		not specified	Uncertain significance (Nov 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PASK	protein_coding	protein_coding	ENST00000358649	17	44166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-21	0.268	124965	2	781	125748	0.00312

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0430	772	769	1.00	0.0000493	8602
Missense in Polyphen		244	273.35	0.89262		3245
Synonymous	-0.480	353	342	1.03	0.0000251	2785
Loss of Function	1.76	40	53.9	0.741	0.00000289	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00386	0.00386
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.00190	0.00174
Finnish	0.00273	0.00268
European (Non-Finnish)	0.00445	0.00444
Middle Eastern	0.00190	0.00174
South Asian	0.00170	0.00167
Other	0.00342	0.00343

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase involved in energy homeostasis and protein translation. Phosphorylates EEF1A1, GYS1, PDX1 and RPS6. Probably plays a role under changing environmental conditions (oxygen, glucose, nutrition), rather than under standard conditions. Acts as a sensor involved in energy homeostasis: regulates glycogen synthase synthesis by mediating phosphorylation of GYS1, leading to GYS1 inactivation. May be involved in glucose-stimulated insulin production in pancreas and regulation of glucagon secretion by glucose in alpha cells; however such data require additional evidences. May play a role in regulation of protein translation by phosphorylating EEF1A1, leading to increase translation efficiency. May also participate to respiratory regulation. {ECO:0000269|PubMed:16275910, ECO:0000269|PubMed:17052199, ECO:0000269|PubMed:17595531, ECO:0000269|PubMed:20943661, ECO:0000269|PubMed:21181396, ECO:0000269|PubMed:21418524}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.833
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.76

Haploinsufficiency Scores

• pHI: 0.499
• hipred: N
• hipred_score: 0.173
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.761

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pask
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein phosphorylation;intracellular signal transduction;regulation of respiratory gaseous exchange;negative regulation of glycogen biosynthetic process;positive regulation of translation;protein autophosphorylation;regulation of glucagon secretion;energy homeostasis
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;phosphatidylinositol binding