rs587784366

Positions:

• chr19-49861765-ACGCTACCTGG-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_007254.4(PNKP):​c.1295_1298+6del variant causes a splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000046 in 1,566,646 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. A432A) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000047 (0 hom.)
• Consequence: PNKP NM_007254.4 splice_donor, splice_donor_5th_base, coding_sequence, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 3.56

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]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 5, offset of 19, new splice context is: gccGTaggt. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-49861765-ACGCTACCTGG-A is Pathogenic according to our data. Variant chr19-49861765-ACGCTACCTGG-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 159788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PNKP	NM_007254.4	c.1295_1298+6del		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	14/17	ENST00000322344.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PNKP	ENST00000322344.8	c.1295_1298+6del		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	14/17	1	NM_007254.4	P1

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 152120 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000683 AC: 12 AN: 175710 Hom.: 0 AF XY: 0.0000848 AC XY: 8 AN XY: 94316

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000286

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000685

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000474 AC: 67 AN: 1414526 Hom.: 0 AF XY: 0.0000586 AC XY: 41 AN XY: 699848

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000296

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000349

Gnomad4 OTH exome AF: 0.0000854

GnomAD4 genome AF: 0.0000329 AC: 5 AN: 152120 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74298

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000434 Hom.: 0

Bravo AF: 0.0000227

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Apr 06, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 19, 2013	The c.1295_1298+6delCCAGGTAGCG mutation in the PNKP gene results in the deletion of ten nucleotides at the exon 14/intron 14 boundary, thereby destroying the canonical splice donor site in intron 14. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product if the message is used for protein translation. Although this mutation has not been previously reported to our knowledge, it is considered a disease-causing mutation.The variant is found in CHILD-EPI,EPILEPSY panel(s). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 28, 2016	- -

Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Dec 19, 2023

The c.1295_1298+6del (NM_007254.3 c.1295_1298+6delCCAGGTAGCG) variant in PNKP has been reported in the compound heterozygous state in 1 individual with microcephaly with early onset seizures (MCSZ), in 1 individual with motor neuropathy, and in 2 individuals with ataxia with oculomotor apraxia and segregated with disease in 2 affected relatives from 1 family (Previtali 2019 PMID: 31167812, Kalasova 2019 PMID: 31041400, da Costa 2022 PMID: 35426160). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 159788) and has been identified in 0.06% (3/4832) of South Asian and 0.0029% (2/68006) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). This variant is a deletion of ten nucleotides at the exon 14/intron 14 boundary, thereby destroying the canonical splice donor site in intron 14. It is predicted to cause altered splicing, leading to an abnormal or absent protein. Biallelic loss of function of the PNKP gene has been associated with ataxia with oculomotor apraxia. Functional studies in patient fibroblasts provide some evidence that this variant reduced protein expression and activity and were more susceptible to single strand breaks due to reduced repair activity (Kalasova 2019 PMID: 31041400, Kalasova 2020 PMID: 32504494). In summary, the c.1295_1298+6delCCAGGTAGCG variant in PNKP meets criteria to be classified as pathogenic for PNKP-related disorders, such as autosomal recessive ataxia with oculomotor apraxia, and autosomal recessive microcephaly, seizures and developmental delay. ACMG/AMP Criteria applied: PVS1, PM3_Strong, PP1, PS3_Supporting. -

Microcephaly, seizures, and developmental delay Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jun 05, 2014

- -

PNKP-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jun 06, 2024

Variant summary: PNKP c.1295_1298+6del10 is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site. The variant allele was found at a frequency of 6.8e-05 in 175710 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in PNKP causing PNKP-Related Disorders, allowing no conclusion about variant significance. The variant, c.1295_1298+6del10, has been reported in the literature in multiple individuals affected with PNKP-Related Disorders ranging from microcephaly with early onset seizures to oculomotor apraxia and Charcot-Marie-Tooth type 2 (CMT2) disease (e.g. Previtali_2019, Kalasova_2020, daCosta_2022). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, and demonstrated strongly reduced protein level and reduced function in patient derived cells (Kalasova_2020). The following publications have been ascertained in the context of this evaluation (PMID: 31167812, 32504494, 35426160). ClinVar contains an entry for this variant (Variation ID: 159788). Based on the evidence outlined above, the variant was classified as pathogenic. -

Developmental and epileptic encephalopathy, 12 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 04, 2023

This variant results in the deletion of part of exon 14 (c.1295_1298+6del) of the PNKP gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PNKP are known to be pathogenic (PMID: 20118933, 25728773). This variant is present in population databases (rs587784366, gnomAD 0.03%). This variant has been observed in individual(s) with PNKP-related conditions (PMID: 31167812). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 159788). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects PNKP function (PMID: 32504494). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587784366; hg19: chr19-50365022;