chr3-196806648-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002577.4(PAK2):c.538C>T(p.Pro180Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002577.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAK2 | NM_002577.4 | c.538C>T | p.Pro180Ser | missense_variant | Exon 6 of 15 | ENST00000327134.7 | NP_002568.2 | |
PAK2 | XM_011512870.3 | c.538C>T | p.Pro180Ser | missense_variant | Exon 6 of 15 | XP_011511172.1 | ||
PAK2 | XM_047448218.1 | c.538C>T | p.Pro180Ser | missense_variant | Exon 6 of 15 | XP_047304174.1 | ||
PAK2 | XM_047448219.1 | c.538C>T | p.Pro180Ser | missense_variant | Exon 6 of 15 | XP_047304175.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251322Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135848
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460484Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 726646
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.538C>T (p.P180S) alteration is located in exon 6 (coding exon 5) of the PAK2 gene. This alteration results from a C to T substitution at nucleotide position 538, causing the proline (P) at amino acid position 180 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at