PANK4

pantothenate kinase 4 (inactive), the group of Pantothenate kinase family

Basic information

Region (hg38): 1:2508537-2526597

Links

ENSG00000157881 ∙ NCBI:55229 ∙ OMIM:606162 ∙ HGNC:19366 ∙ Uniprot:Q9NVE7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• early-onset posterior polar cataract (Supportive), mode of inheritance: AD
• cataract 49 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 49	AD	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	Ophthalmologic	30585370

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PANK4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PANK4 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				4	1	5
missense			36		1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	4	2

Variants in PANK4

This is a list of pathogenic ClinVar variants found in the PANK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-2508890-C-T		not specified	Likely benign (May 13, 2024)
1-2508953-C-T		not specified	Uncertain significance (Mar 19, 2024)
1-2508964-G-A			Likely benign (May 01, 2022)
1-2509013-T-A		not specified	Uncertain significance (Dec 19, 2022)
1-2509035-G-C		not specified	Uncertain significance (Sep 27, 2024)
1-2509869-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-2510061-C-A		not specified	Uncertain significance (Oct 12, 2021)
1-2510061-C-T		not specified	Uncertain significance (Jan 10, 2022)
1-2510078-G-A		not specified	Uncertain significance (Oct 20, 2021)
1-2510129-G-A		not specified	Uncertain significance (Aug 14, 2024)
1-2510686-C-G		not specified	Uncertain significance (Jun 30, 2023)
1-2510695-G-C		not specified	Uncertain significance (Jun 12, 2023)
1-2510703-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-2510767-A-C		not specified	Uncertain significance (Apr 28, 2022)
1-2512898-C-T		not specified	Uncertain significance (Jun 05, 2024)
1-2512913-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-2512969-C-T		not specified	Uncertain significance (Mar 03, 2022)
1-2512975-G-A		Cataract 49	Benign (Apr 11, 2023)
1-2512976-C-A		not specified	Uncertain significance (Aug 08, 2023)
1-2512987-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-2512988-G-A		not specified	Uncertain significance (Nov 14, 2023)
1-2513018-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-2514088-C-T		not specified	Uncertain significance (Dec 10, 2024)
1-2514372-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-2514429-A-G		not specified	Uncertain significance (Oct 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PANK4	protein_coding	protein_coding	ENST00000378466	19	18068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0168	125670	0	11	125681	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	362	517	0.701	0.0000355	5019
Missense in Polyphen		91	203.62	0.44691		2116
Synonymous	-2.13	280	238	1.18	0.0000188	1541
Loss of Function	4.89	6	38.9	0.154	0.00000191	443

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000587	0.0000587
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000538	0.0000528
Middle Eastern	0.0000550	0.0000544
South Asian	0.0000327	0.0000327
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: 0.122

Intolerance Scores

• loftool: 0.0792
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.95

Haploinsufficiency Scores

• pHI: 0.128
• hipred: Y
• hipred_score: 0.625
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pank4

Gene ontology

• Biological process: coenzyme A biosynthetic process;phosphorylation
• Cellular component: cytoplasm
• Molecular function: pantothenate kinase activity;ATP binding