PANK1

pantothenate kinase 1, the group of MicroRNA protein coding host genes|Pantothenate kinase family

Basic information

Region (hg38): 10:89579497-89645242

Previous symbols: [ "PANK" ]

Links

ENSG00000152782

∙ NCBI:53354 ∙ OMIM:606160 ∙ HGNC:8598 ∙ Uniprot:Q8TE04 ∙ 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 PANK1 gene.

not_specified (27 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PANK1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000148977.3. 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						0
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PANK1	protein_coding	protein_coding	ENST00000307534	7	62471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00268	0.995	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	238	318	0.749	0.0000167	3835
Missense in Polyphen		93	164.87	0.56408		1889
Synonymous	0.270	131	135	0.970	0.00000749	1223
Loss of Function	2.63	8	21.0	0.381	0.00000116	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.0000904
Ashkenazi Jewish	0.000875	0.000794
East Asian	0.0000544	0.0000544
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.0000544	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000672	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role in the physiological regulation of the intracellular CoA concentration. {ECO:0000250}.;
Pathway: Pantothenate and CoA biosynthesis - Homo sapiens (human);Glycolysis;Glycogenosis, Type VII. Tarui disease;Gluconeogenesis;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Fanconi-bickel syndrome;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Pantothenate and CoA Biosynthesis;Glycogenosis, Type IB;Coenzyme A biosynthesis;Metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;coenzyme A biosynthesis (Consensus)

Recessive Scores

pRec: 0.119

Intolerance Scores

loftool: 0.213
rvis_EVS: 0.28
rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

pHI: 0.546
hipred: N
hipred_score: 0.464
ghis: 0.400

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pank1
Phenotype: growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype;

Gene ontology

Biological process: coenzyme biosynthetic process;coenzyme A biosynthetic process;phosphorylation
Cellular component: cytosol;cell periphery
Molecular function: pantothenate kinase activity;ATP binding;protein homodimerization activity;acetyl-CoA binding