rs749527505
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006904.7(PRKDC):c.7331C>T(p.Pro2444Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000306 in 1,599,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P2444S) has been classified as Uncertain significance.
Frequency
Consequence
NM_006904.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKDC | NM_006904.7 | c.7331C>T | p.Pro2444Leu | missense_variant | 55/86 | ENST00000314191.7 | |
PRKDC | NM_001081640.2 | c.7331C>T | p.Pro2444Leu | missense_variant | 55/85 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKDC | ENST00000314191.7 | c.7331C>T | p.Pro2444Leu | missense_variant | 55/86 | 1 | NM_006904.7 | P1 | |
PRKDC | ENST00000338368.7 | c.7331C>T | p.Pro2444Leu | missense_variant | 55/85 | 1 | |||
PRKDC | ENST00000697603.1 | c.8C>T | p.Pro3Leu | missense_variant | 2/33 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000878 AC: 2AN: 227916Hom.: 0 AF XY: 0.00000814 AC XY: 1AN XY: 122810
GnomAD4 exome AF: 0.0000318 AC: 46AN: 1447778Hom.: 0 Cov.: 30 AF XY: 0.0000223 AC XY: 16AN XY: 718732
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to DNA-PKcs deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at