STAG2 c.1240dupT, p.Tyr414LeufsTer27
NM_001042749.1:c.1240dupT
COSM6964604
Population Frequency
0.0 in 100,000
Rare
ClinVar Classification
Unknown
0 publications
REVEL Score
N/A
Not Available
COSMIC Recurrence
1 occurrences
No Criteria Applied
Classification Evidence
Detailed Information
Genetic Information
Gene & Transcript Details
Gene
STAG2
Transcript
NM_001042749.2
Total Exons
35
Strand
Forward (+)
Reference Sequence
NC_000023.10
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_001042749.1 | Alternative | 35 exons | Forward |
Variant Details
HGVS Notation
NM_001042749.1:c.1240dupT
Protein Change
Y414Lfs*27
Location
Exon 14
(Exon 14 of 35)
5'
Exon Structure (35 total)
3'
Functional Consequence
Loss of Function
Related Variants
No evidence of other pathogenic variants at position 414 in gene STAG2
Alternate Identifiers
COSM6964604
Variant interpretation based on transcript NM_001042749.2
Clinical Evidence
Population Frequency
Global Frequency
0.0 in 100,000
Extremely Rare
Global: 0.0%
0%
0.0005%
0.001%
0.01%
0.05%
1%+
ACMG Criteria Applied
PM2
This variant is rare in the population (0.000000% MAF).
Classification
Unknown
Publications
0 publications
Clinical Statement
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain (0 mutations).
Related Variants in This Domain
No evidence of other pathogenic variants at position 414 in gene STAG2
Functional Studies
Summary
The variant STAG2 Y414Lfs*27 has not been functionally characterized in the provided sources.
Computational Evidence
Pathogenicity Predictions
Predictor Consensus
Unknown
PP3 Applied
No
VCEP Guidelines
Applied ACMG/AMP Criteria
PVS1
PVS1 (Very Strong)
According to VCEP guidelines: 'PVS1 – Null variant in a gene where loss of function (LoF) is a known mechanism of disease.' The evidence for this variant shows: It is a truncating variant (Y414Lfs*27) in the STAG2 gene, where loss of function is a known mechanism of disease. Therefore, this criterion meets the requirements because the variant is predicted to result in a loss of function.
PM2
PM2 (Moderate)
According to VCEP guidelines: 'PM2 – Absent from controls (or at extremely low frequency if recessive).' The evidence for this variant shows: The variant is not found in population databases such as gnomAD, indicating it is absent from controls. Therefore, this criterion meets the requirements because the variant is not present in the general population.