17-39212326-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_198993.5(STAC2):c.1202G>A(p.Gly401Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000616 in 1,459,926 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
Consequence
NM_198993.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STAC2 | NM_198993.5 | c.1202G>A | p.Gly401Asp | missense_variant | Exon 11 of 11 | ENST00000333461.6 | NP_945344.1 | |
STAC2 | NM_001351360.2 | c.776G>A | p.Gly259Asp | missense_variant | Exon 11 of 11 | NP_001338289.1 | ||
STAC2 | XM_017024580.2 | c.1217G>A | p.Gly406Asp | missense_variant | Exon 11 of 11 | XP_016880069.1 | ||
STAC2 | XM_017024581.2 | c.1052G>A | p.Gly351Asp | missense_variant | Exon 9 of 9 | XP_016880070.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STAC2 | ENST00000333461.6 | c.1202G>A | p.Gly401Asp | missense_variant | Exon 11 of 11 | 1 | NM_198993.5 | ENSP00000327509.5 | ||
STAC2 | ENST00000584501.1 | n.*553G>A | non_coding_transcript_exon_variant | Exon 11 of 11 | 1 | ENSP00000463299.1 | ||||
STAC2 | ENST00000584501.1 | n.*553G>A | 3_prime_UTR_variant | Exon 11 of 11 | 1 | ENSP00000463299.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245480Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133070
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1459926Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 726048
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1202G>A (p.G401D) alteration is located in exon 11 (coding exon 11) of the STAC2 gene. This alteration results from a G to A substitution at nucleotide position 1202, causing the glycine (G) at amino acid position 401 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