PANK2

pantothenate kinase 2, the group of Pantothenate kinase family|MicroRNA protein coding host genes

Basic information

Region (hg38): 20:3888839-3929887

Previous symbols: [ "C20orf48", "NBIA1" ]

Links

ENSG00000125779

∙ NCBI:80025 ∙ OMIM:606157 ∙ HGNC:15894 ∙ Uniprot:Q9BZ23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

pantothenate kinase-associated neurodegeneration (Strong), mode of inheritance: AR
pantothenate kinase-associated neurodegeneration (Strong), mode of inheritance: AR
pantothenate kinase-associated neurodegeneration (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration; Neurodegeneration with brain iron accumulation 1	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal; Hematologic; Neurologic; Ophthalmologic	477009; 7158329; 3969211; 1447570; 1734303; 7885538; 7898702; 8944032; 11479594; 12058097; 12510040; 14638969; 15911822; 15642932; 16240131; 16437574; 16687521; 18981035; 20301663; 21286947

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PANK2 gene.

Pigmentary_pallidal_degeneration (516 variants)
not_provided (109 variants)
Inborn_genetic_diseases (58 variants)
not_specified (21 variants)
Hypoprebetalipoproteinemia,_acanthocytosis,_retinitis_pigmentosa,_and_pallidal_degeneration (14 variants)
PANK2-related_disorder (10 variants)
Retinitis_pigmentosa (3 variants)
Dystonic_disorder (2 variants)
See_cases (2 variants)
Neurodegeneration (2 variants)
Leber_congenital_amaurosis (1 variants)
Cone-rod_dystrophy (1 variants)
Optic_atrophy (1 variants)
Rubinstein-Taybi_syndrome_due_to_EP300_haploinsufficiency (1 variants)
Retinal_dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PANK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001386393.1. 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				168 clinvar	1 clinvar	169
missense	18 clinvar	47 clinvar	164 clinvar	6 clinvar		235
nonsense	16 clinvar	1 clinvar	3 clinvar			20
start loss						0
frameshift	33 clinvar	14 clinvar				47
splice donor/acceptor (+/-2bp)	6 clinvar	8 clinvar		1 clinvar		15
Total	73	70	167	175	1

Highest pathogenic variant AF is 0.000244726

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PANK2	protein_coding	protein_coding	ENST00000316562	7	38120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.40e-7	0.909	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.179	298	307	0.971	0.0000165	3576
Missense in Polyphen		50	88.235	0.56667		1021
Synonymous	-2.36	163	129	1.26	0.00000696	1224
Loss of Function	1.68	13	21.4	0.608	0.00000111	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000380	0.000380
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000248	0.000246
Middle Eastern	0.000272	0.000272
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May be the master regulator of the CoA biosynthesis. {ECO:0000250}.;
Disease: DISEASE: Hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration (HARP) [MIM:607236]: Rare syndrome with many clinical similarities to PKAN. {ECO:0000269|PubMed:12058097}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Pantothenate and CoA biosynthesis - Homo sapiens (human);Coenzyme A biosynthesis;Vitamin B5 - CoA biosynthesis from pantothenate;Metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;coenzyme A biosynthesis (Consensus)

Recessive Scores

pRec: 0.192

Intolerance Scores

loftool: 0.132
rvis_EVS: -0.23
rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

pHI: 0.461
hipred: N
hipred_score: 0.446
ghis: 0.594

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pank2
Phenotype: renal/urinary system phenotype; immune system phenotype; vision/eye 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); reproductive 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); hematopoietic system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: pank2
Affected structure: nucleate erythrocyte
Phenotype tag: abnormal
Phenotype quality: spatial pattern

Gene ontology

Biological process: spermatid development;aerobic respiration;coenzyme biosynthetic process;coenzyme A biosynthetic process;pantothenate metabolic process;phosphorylation;regulation of fatty acid metabolic process;regulation of mitochondrial membrane potential;mitochondrion morphogenesis;regulation of triglyceride metabolic process;regulation of bile acid metabolic process
Cellular component: nucleus;mitochondrion;mitochondrial intermembrane space;cytosol
Molecular function: pantothenate kinase activity;ATP binding