1-167117457-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080426.3(STYXL2):c.335C>T(p.Thr112Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000409 in 1,612,492 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.335C>T | p.Thr112Met | missense_variant | Exon 4 of 6 | 5 | NM_001080426.3 | ENSP00000354483.2 | ||
STYXL2 | ENST00000271385.9 | c.335C>T | p.Thr112Met | missense_variant | Exon 4 of 6 | 1 | ENSP00000271385.5 | |||
STYXL2 | ENST00000443333.1 | c.335C>T | p.Thr112Met | missense_variant | Exon 3 of 5 | 5 | ENSP00000404874.1 | |||
GPA33 | ENST00000632571.1 | c.-281-43918G>A | intron_variant | Intron 1 of 3 | 4 | ENSP00000488407.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000141 AC: 35AN: 247452Hom.: 0 AF XY: 0.000157 AC XY: 21AN XY: 133640
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1460288Hom.: 0 Cov.: 31 AF XY: 0.0000427 AC XY: 31AN XY: 726192
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.335C>T (p.T112M) alteration is located in exon 3 (coding exon 3) of the DUSP27 gene. This alteration results from a C to T substitution at nucleotide position 335, causing the threonine (T) at amino acid position 112 to be replaced by a methionine (M). 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