GeneBe

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.

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.

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
16
clinvar
 16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
2
clinvar
1
clinvar
 3
Total 0 0 18 0 1

Variants in PANK1

This is a list of pathogenic ClinVar variants found in the PANK1 region.

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

Position Type Phenotype Significance ClinVar
10-89588723-T-A not specified Uncertain significance (Mar 25, 2024)3304182
10-89588762-C-T not specified Uncertain significance (Nov 10, 2024)3413840
10-89593265-C-T not specified Uncertain significance (May 01, 2024)2392422
10-89593288-T-C not specified Uncertain significance (Aug 05, 2024)3413842
10-89593306-A-T not specified Uncertain significance (Dec 02, 2024)3413843
10-89593820-C-T not specified Uncertain significance (Jun 13, 2023)2560091
10-89593862-C-T Uncertain significance (Jun 01, 2023)2640669
10-89599486-T-C not specified Uncertain significance (Mar 14, 2023)2496001
10-89611728-C-T not specified Uncertain significance (Jul 20, 2021)2238873
10-89611823-A-C not specified Uncertain significance (Mar 08, 2024)3208326
10-89611823-A-G not specified Uncertain significance (Mar 23, 2022)2279768
10-89611853-A-G not specified Uncertain significance (Dec 12, 2023)3208325
10-89611932-G-A not specified Uncertain significance (Aug 20, 2024)2264934
10-89611940-T-C not specified Uncertain significance (Feb 26, 2025)3885451
10-89611948-C-A not specified Uncertain significance (Oct 09, 2024)3413841
10-89611971-C-T not specified Uncertain significance (May 02, 2024)3304183
10-89644840-C-A not specified Uncertain significance (Sep 27, 2021)2252650
10-89644972-C-T Benign (Aug 02, 2017)768376
10-89645089-C-A not specified Uncertain significance (Sep 16, 2021)2400168
10-89645206-G-A not specified Uncertain significance (Aug 13, 2021)2244589

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PANK1protein_codingprotein_codingENST00000307534 762471
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.002680.9951257270211257480.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.592383180.7490.00001673835
Missense in Polyphen93164.870.564081889
Synonymous0.2701311350.9700.000007491223
Loss of Function2.63821.00.3810.00000116249

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001270.0000904
Ashkenazi Jewish0.0008750.000794
East Asian0.00005440.0000544
Finnish0.00004720.0000462
European (Non-Finnish)0.00005440.0000527
Middle Eastern0.00005440.0000544
South Asian0.00006720.0000653
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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