chr19-49862369-A-G

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5

The NM_007254.4(PNKP):c.1029+2T>C variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,280,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0019 ( 0 hom. )

Consequence

PNKP
NM_007254.4 splice_donor, intron

Scores

Splicing: ADA: 1.000

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:22U:4

Conservation

PhyloP100: 3.19

Variant links:

Genes affected

PNKP (HGNC:9154): (polynucleotide kinase 3'-phosphatase) This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]

PNKP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.059386972 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 19-49862369-A-G is Pathogenic according to our data. Variant chr19-49862369-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 206401.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=8, Uncertain_significance=4, Pathogenic=9}. Variant chr19-49862369-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PNKP	NM_007254.4 link	c.1029+2T>C		splice_donor_variant, intron_variant	Intron 11 of 16	ENST00000322344.8	NP_009185.2	Q96T60-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNKP	ENST00000322344.8 link	c.1029+2T>C		splice_donor_variant, intron_variant	Intron 11 of 16	1	NM_007254.4	ENSP00000323511.2		Q96T60-1

Frequencies

GnomAD3 genomes

AF:

0.00109

AC:

157

AN:

144138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000203

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.000602

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000236

Gnomad FIN

AF:

0.00200

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00195

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00106

AC:

158

AN:

149072

Hom.:

AF XY:

0.00109

AC XY:

AN XY:

79842

show subpopulations

Gnomad AFR exome

AF:

0.000525

Gnomad AMR exome

AF:

0.000328

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000134

Gnomad FIN exome

AF:

0.00135

Gnomad NFE exome

AF:

0.00212

Gnomad OTH exome

AF:

0.000943

GnomAD4 exome

AF:

0.00187

AC:

2120

AN:

1136252

Hom.:

Cov.:

AF XY:

0.00179

AC XY:

1016

AN XY:

567000

show subpopulations

Gnomad4 AFR exome

AF:

0.000156

Gnomad4 AMR exome

AF:

0.000385

Gnomad4 ASJ exome

AF:

0.000139

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000674

Gnomad4 FIN exome

AF:

0.00130

Gnomad4 NFE exome

AF:

0.00229

Gnomad4 OTH exome

AF:

0.00145

GnomAD4 genome

AF:

0.00109

AC:

157

AN:

144240

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

AN XY:

70546

show subpopulations

Gnomad4 AFR

AF:

0.000202

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.000602

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000237

Gnomad4 FIN

AF:

0.00200

Gnomad4 NFE

AF:

0.00195

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00182

Hom.:

Bravo

AF:

0.000854

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00123

AC:

ExAC

AF:

0.000272

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:22Uncertain:4

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Microcephaly, seizures, and developmental delay

Pathogenic:8Uncertain:1

Feb 05, 2022

DASA

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1029+2T>C variant is located in a canonical splice-site, and it is not predicted the protein reading frame alteration, however, occur in a critical region and the variant disrupts <10% of protein - PVS1_moderate. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 206401; PMID: 33654647, 31061747) - PS4_moderate. The variant is present at low allele frequencies population databases (rs199919568 – gnomAD 0.01089%; ABraOM 0.001281 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The c.1029+2T>C was detected in trans with a pathogenic variant (PMID: 31061747; 33654647) - PM3. The variant co-segregated with disease in multiple affected family members (PMID: 31061747) - PP1. In summary, the currently available evidence indicates that the variant is likely pathogenic. -

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was identified as compound heterozygous. -

May 31, 2017

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 10, 2022

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Oct 10, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with ataxia-oculomotor apraxia 4 (MIM#616267), and microcephaly, seizures, and developmental delay (MIM#613402). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). It has been suggested that this variant cases exon 11 skipping however, the relevant data was not shown (PMID: 32123317). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (190 heterozygotes, 0 homozygotes). (SP) 0311 - Multiple alternative nucleotide changes at the same canonical splice site are present in gnomAD (v4) (highest allele count: 2 heterozygotes, 0 homozygotes. (I) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0704 - Another canonical splice site variant comparable to the one identified in this case has limited previous evidence for pathogenicity. A different variant in the same splice site (c.1029+1G>A) has been reported as pathogenic (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has been classified as pathogenic or likely pathogenic by multiple clinical laboratories in ClinVar and has been observed as compound heterozygous in six individuals from four families with ataxia-culomotor apraxia (PMIDs: 31061747, 33654647, 34697416). It has also been classified as a VUS or likely benign in ClinVar, but these submissions do not contain significant justification for the classification and are outweighed by the pathogenic and likely pathogenic submissions. (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Jul 28, 2017

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 02, 2023

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

The heterozygous c.1029+2T>C variant in PNKP was identified by our study in 1 individual with microcephaly, seizures, and intellectual disability (Broad Institute Rare Genomes Project). The significance of the c.1029+2T>C variant is uncertain. If you have any additional information about functional evidence we encourage you to reach out to us. -

Oct 09, 2023

Zotz-Klimas Genetics Lab, MVZ Zotz Klimas

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 01, 2015

Genetic Services Laboratory, University of Chicago

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Pathogenic:7Uncertain:1

Dec 27, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 30, 2022

Revvity Omics, Revvity

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PNKP: PM3:Strong, PP1:Strong, PVS1:Strong, PM2:Supporting -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 19, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM3, PS3_moderate, PVS1_strong -

Nov 01, 2018

Athena Diagnostics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 25, 2025

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

RNA studies and functional RNA analyses demonstrate a damaging effect and indicate aberrant splicing in response to c.1029+2T>C resulting predominately in skipping of exon 11, affecting the phosphatase domain and the kinase domain (PMID: 37301908, 34697416, 22508754); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 31061747, 29655203, 29720203, 29261713, 22508754, 32123317, 34697416, Fontaine2022[Preprint], 33654647, 37301908, 38523675) -

Ataxia - oculomotor apraxia type 4

Pathogenic:2

Apr 02, 2020

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2. -

Oct 02, 2020

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -

Inborn genetic diseases

Pathogenic:1

Jan 05, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1029+2T>C intronic variant results from a T to C substitution two nucleotides after exon 11 (coding exon 10) of the PNKP gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, direct evidence is unavailable. Based on data from gnomAD, the PNKP c.1029+2T>C alteration has an overall frequency of 0.11% (190/178830) total alleles studied. The highest observed frequency was 0.21% (147/70858) of European (non-Finnish) alleles. This alteration has been reported in the compound heterozygous state in individuals with a spectrum of presentations including PNKP-related neurodevelopmental disorder and ataxia-oculomotor apraxia 4 (AOA4) (Freitas, 2021; Rudenskaya, 2019). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the available evidence, this alteration is classified as pathogenic. -

Abnormal cerebral morphology

Pathogenic:1

Diagnostic Laboratory, Strasbourg University Hospital

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease type 2B2;C3150667:Microcephaly, seizures, and developmental delay;C4225397:Ataxia - oculomotor apraxia type 4

Pathogenic:1

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been reported in the literature in the compound heterozygous state in at least 2 individuals with features of ataxia with oculomotor apraxia type 4 (AOA4) segregating with disease in 2 affected family members. This variant has also been identified in the heterozygous state in at least 3 individuals with epilepsy; however, at least 1 author has called into question the pathogenicity of this variant (Coll 2017 PMID:29261713, Stanek 2018 PMID:29720203, Lindy 2018 PMID:29655203, Rudenskaya 2019 PMID:310617747, Freitas 2021 PMID:33654647). This variant is present in the Genome Aggregation Database (Highest reported MAF 0.2% (127/65136) (https://gnomad.broadinstitute.org/variant/19-49862369-A-G?dataset=gnomad_r3). This variant is present in ClinVar, with several labs classifying this variant as Pathogenic or Likely Pathogenic; however, at least 1 laboratory has submitted a classification of Likely Benign for this variant (Variation ID:206401). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. RNA studies predict that this variant will impact the protein with altered splicing (Wai 2020 PMID:32123317). However, these studies may not accurately represent in vivo biological function. Of note, this variant alters the consensus splice sequence (+/- 1,2) which is predicted to result in an absent or abnormal protein. Loss of function variants are a known mechanism of disease for this gene (Dumitrache 2017 PMID:27125728). However, this variant is expected to alter exon 11; this exon is in frame and represents less than 10% of the total protein. In summary, data on this variant is highly suspicious for disease, but requires further evidence for pathogenicity. Therefore, this variant is classified as likely pathogenic. -

Developmental and epileptic encephalopathy, 12

Pathogenic:1

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 11 of the PNKP gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs199919568, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individual(s) with clinical features of PNKP-related conditions (PMID: 31061747). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 206401). Studies have shown that disruption of this splice site results in skipping of exon 11 and/or intron 10 retention , and produces a non-functional protein and/or introduces a premature termination codon (PMID: 34697416, 37301908). For these reasons, this variant has been classified as Pathogenic. -

Microcephaly, seizures, and developmental delay;C4225397:Ataxia - oculomotor apraxia type 4

Pathogenic:1

Feb 13, 2023

Genetics and Molecular Pathology, SA Pathology

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Uncertain:1

Jun 24, 2020

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant classified as Uncertain Significance - Favor Pathogenic. The c.1029+2T>C variant in PNKP has been reported in the compound heterozygous state in one individual with Ataxia with Oculomotor Apraxia Type 4 and their affected sibling (Rudenskaya 2019 PMID: 31061747). It has also been identified in 3 individuals with epilepsy (Lindy 2018 PMID: 29655203, Stanek 2018 PMID: 29720203, Coll 2017 PMID: 29261713). It has also been reported by other clinical laboratories in ClinVar (Variation ID:206401) and has been identified in 0.2% (147/70858) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. However, exon 11, which is affected by this variant, is in frame and consists of only 93 base pairs and encodes less than 10% of the PNKP protein. The PNKP gene has been definitively been associated with autosomal recessive ataxia with oculomotor apraxia and with microcephaly, seizures, and developmental delay. However, there is limited evidence regarding its association with epilepsy. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain for autosomal recessive ataxia with oculomotor apraxia. ACMG/AMP Criteria applied: PVS1_Moderate, PM3, PP1_Supporting. -

PNKP-related disorder

Uncertain:1

Feb 12, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The PNKP c.1029+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in the compound heterozygous state in at least five individuals with severe progressive microcephaly, hypotonia, developmental delays, and ataxia-oculomotor apraxia type 4 (Neuser et al. 2021. PubMed ID: 34697416; Rudenskaya et al. 2019. PubMed ID: 31061747; Freitas et al. 2021. PubMed ID: 33654647). Functional studies confirm that this variant causes aberrant splicing by skipping exon 11, resulting in an in-frame deletion of amino acids 313-343 (Wai et al. 2020. PubMed ID: 32123317). This variant is reported in 0.21% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations regarding it pathogenicity in ClinVar, ranging from pathogenic to likely pathogenic to uncertain significance to likely benign (https://www.ncbi.nlm.nih.gov/clinvar/variation/206401/). Loss of function is a known mechanism of disease for PNKP, and other splice altering changes have been reported as causative; however these other pathogenic variants are all found at lower frequency in gnomAD (Human Gene Mutation Database). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.30

BayesDel_noAF

Uncertain

0.050

CADD

Uncertain

DANN

Uncertain

0.99

Eigen

Pathogenic

0.96

Eigen_PC

Pathogenic

0.78

FATHMM_MKL

Uncertain

0.92

GERP RS

5.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.93

SpliceAI score (max)

0.93

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.93

Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over