1-167117484-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080426.3(STYXL2):c.362C>A(p.Ala121Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000546 in 1,612,114 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080426.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STYXL2 | ENST00000361200.7 | c.362C>A | p.Ala121Asp | missense_variant | Exon 4 of 6 | 5 | NM_001080426.3 | ENSP00000354483.2 | ||
STYXL2 | ENST00000271385.9 | c.362C>A | p.Ala121Asp | missense_variant | Exon 4 of 6 | 1 | ENSP00000271385.5 | |||
STYXL2 | ENST00000443333.1 | c.362C>A | p.Ala121Asp | missense_variant | Exon 3 of 5 | 5 | ENSP00000404874.1 | |||
GPA33 | ENST00000632571.1 | c.-281-43945G>T | intron_variant | Intron 1 of 3 | 4 | ENSP00000488407.1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000851 AC: 21AN: 246688Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133222
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1459916Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 725926
GnomAD4 genome AF: 0.000283 AC: 43AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.362C>A (p.A121D) alteration is located in exon 3 (coding exon 3) of the DUSP27 gene. This alteration results from a C to A substitution at nucleotide position 362, causing the alanine (A) at amino acid position 121 to be replaced by an aspartic acid (D). 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