rs576363906
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM4PP3BP6_Very_StrongBS2
The NM_015488.5(PNKD):βc.1140_1145delβ(p.Met381_His382del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,613,744 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (β β ).
Frequency
Genomes: π 0.00070 ( 0 hom., cov: 33)
Exomes π: 0.0012 ( 3 hom. )
Consequence
PNKD
NM_015488.5 inframe_deletion
NM_015488.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.02
Genes affected
PNKD (HGNC:9153): (PNKD metallo-beta-lactamase domain containing) This gene is thought to play a role in the regulation of myofibrillogenesis. Mutations in this gene have been associated with the movement disorder paroxysmal non-kinesigenic dyskinesia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_015488.5.
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
BP6
Variant 2-218344961-GATATGC-G is Benign according to our data. Variant chr2-218344961-GATATGC-G is described in ClinVar as [Likely_benign]. Clinvar id is 334329.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218344961-GATATGC-G is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | c.1140_1145del | p.Met381_His382del | inframe_deletion | 10/10 | ENST00000273077.9 | |
CATIP-AS2 | NR_125777.1 | n.120+6193_120+6198del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNKD | ENST00000273077.9 | c.1140_1145del | p.Met381_His382del | inframe_deletion | 10/10 | 1 | NM_015488.5 | ||
CATIP-AS2 | ENST00000411433.1 | n.120+6193_120+6198del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000703 AC: 107AN: 152138Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000595 AC: 148AN: 248688Hom.: 0 AF XY: 0.000637 AC XY: 86AN XY: 135092
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GnomAD4 exome AF: 0.00119 AC: 1745AN: 1461488Hom.: 3 AF XY: 0.00113 AC XY: 825AN XY: 727044
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GnomAD4 genome AF: 0.000703 AC: 107AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.000618 AC XY: 46AN XY: 74452
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Paroxysmal nonkinesigenic dyskinesia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 15, 2021 | This variant is associated with the following publications: (PMID: 33126486) - |
Paroxysmal nonkinesigenic dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
PNKD-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 11, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at