chr2-218270540-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_015488.5(PNKD):​c.5C>T​(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000277 in 1,081,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

PNKD
NM_015488.5 missense

Scores

9
4
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.29
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.768

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PNKDNM_015488.5 linkuse as main transcriptc.5C>T p.Ala2Val missense_variant 1/10 ENST00000273077.9 NP_056303.3
PNKDNM_001077399.3 linkuse as main transcriptc.5C>T p.Ala2Val missense_variant 1/3 NP_001070867.1
PNKDXM_017003771.2 linkuse as main transcriptc.5C>T p.Ala2Val missense_variant 1/9 XP_016859260.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PNKDENST00000273077.9 linkuse as main transcriptc.5C>T p.Ala2Val missense_variant 1/101 NM_015488.5 ENSP00000273077 Q8N490-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000277
AC:
3
AN:
1081158
Hom.:
0
Cov.:
17
AF XY:
0.00000385
AC XY:
2
AN XY:
519496
show subpopulations
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000339
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
ExAC
AF:
0.0000182
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 21, 2023The c.5C>T (p.A2V) alteration is located in exon 1 (coding exon 1) of the PNKD gene. This alteration results from a C to T substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.58
BayesDel_addAF
Pathogenic
0.32
D
BayesDel_noAF
Pathogenic
0.23
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.15
.;T
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.52
FATHMM_MKL
Benign
0.48
N
LIST_S2
Benign
0.85
T;T
M_CAP
Uncertain
0.15
D
MetaRNN
Pathogenic
0.77
D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Benign
0.69
N;N
MutationTaster
Benign
0.82
D;D
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
-0.71
N;N
REVEL
Uncertain
0.49
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
1.0
D;D
Vest4
0.58
MutPred
0.38
Gain of sheet (P = 0.0266);Gain of sheet (P = 0.0266);
MVP
0.91
MPC
0.34
ClinPred
0.95
D
GERP RS
5.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.1
Varity_R
0.49
gMVP
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs764107923; hg19: chr2-219135263; API