Developmental Brain Disorder Gene Database

LoF Variant Gene

Gene
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AR

PNKP

HGNC:9154 (protein-coding gene)

polynucleotide kinase 3'-phosphatase

Unique Cases:
5
Disorders:
ID, EP, CP
Last Updated:
November 4, 2024

Gene Summary:

DBD Genes Classification
PNKP is a High Confidence candidate gene classified as Tier AR. AR genes have autosomal recessive inheritance.
Gene Function
Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways (PubMed:10446192, PubMed:10446193, PubMed:15385968, PubMed:20852255, PubMed:28453785). Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone (PubMed:10446192, PubMed:10446... (Source: Uniprot)
Previous symbols
No previous symbols
Alias symbols
PNK
Chromosomal Location
19q13.33
Genomic Coordinates
GRCh37:chr19:50364460-50370822
GRCh38:chr19:49861204-49867576
Associated Disorders
Intellectual Disability, Epilepsy, Cerebral Palsy

Predictive Scores:

HI Score (Decipher)

59.52

pLI (gnomAD)

0.00

LOEUF (gnomAD)

1.53

Classifications from External Sources:

SFARI Score (SFARI)

Not Scored

DDG2P Classification (DDG2P)

No Classification

ClinGen Classification (ClinGen)

Definitive1

GenCC Classification (GenCC)

Definitive3 Strong3 Supportive3

NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
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