PANK3

pantothenate kinase 3, the group of MicroRNA protein coding host genes|Pantothenate kinase family

Basic information

Region (hg38): 5:168548495-168579368

Links

ENSG00000120137 ∙ NCBI:79646 ∙ OMIM:606161 ∙ HGNC:19365 ∙ Uniprot:Q9H999 ∙ 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 PANK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PANK3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	9	0	1

Variants in PANK3

This is a list of pathogenic ClinVar variants found in the PANK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-168557590-C-T		not specified	Uncertain significance (Sep 08, 2023)
5-168559122-T-A		not specified	Uncertain significance (Jan 23, 2024)
5-168561409-A-G		not specified	Uncertain significance (Mar 18, 2024)
5-168561479-C-T		not specified	Uncertain significance (Oct 26, 2021)
5-168561487-C-T		not specified	Uncertain significance (Mar 14, 2023)
5-168563995-C-G		not specified	Uncertain significance (Oct 13, 2021)
5-168566166-T-C		not specified	Uncertain significance (Aug 28, 2023)
5-168566266-T-C		not specified	Uncertain significance (May 26, 2022)
5-168568786-T-C		not specified	Uncertain significance (Nov 08, 2022)
5-168568965-G-C		not specified	Uncertain significance (Aug 04, 2023)
5-168569008-G-GA			Benign (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PANK3	protein_coding	protein_coding	ENST00000239231	7	31106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000452	0.965	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	95	192	0.494	0.00000963	2395
Missense in Polyphen		37	84.152	0.43968		1058
Synonymous	1.06	60	71.4	0.841	0.00000352	724
Loss of Function	1.91	10	19.0	0.527	0.00000123	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000950	0.0000950
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

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);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: 0.0951

Intolerance Scores

• loftool: 0.398
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.425
• ghis: 0.576

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pank3
• 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)

Gene ontology

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