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.

not_specified (200 variants)
not_provided (29 variants)
PASK-related_disorder (9 variants)
Chronic_kidney_disease (1 variants)

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. These statistics are base on transcript: NM_000015148.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	8 clinvar	16
missense			184 clinvar	24 clinvar	8 clinvar	216
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	185	32	16

Loading clinvar variants...

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