Genetic Information
Gene & Transcript Details
Gene
MSH3
Transcript
NM_002439.5
MANE Select
Total Exons
—
Reference Sequence
NC_000005.9
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_002439.5 | MANE Select | 4443 nt | 77–3490 |
| NM_002439.2 | Alternative | 4645 nt | 254–3667 |
| NM_002439.4 | Alternative | 4472 nt | 81–3494 |
| NM_002439.3 | Alternative | 4645 nt | 254–3667 |
Variant Details
HGVS Notation
NM_002439.5:c.2436-13G>T
Protein Change
?
Location
Exon 17
(Exon 17 of )
17
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
0.0785 in 100,000
Extremely Rare
ACMG Criteria Applied
PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).
ClinVar
OpenClassification
Likely Benign
1 publications
Clinical Statement
"This variant has been reported in ClinVar as Likely benign (3 clinical laboratories)."
COSMIC Somatic Evidence
OpenCOSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
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Functional Impact & Domains
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene MSH3.
Functional Summary
Error in OpenAI Consolidation. OncoKB: MSH32436-13G>TMSH32436-13G>TSomaticNCBI Gene:4437|Show additional gene information Variant OverviewMSH3, a DNA mismatch repair protein, is frequently mutated in colorectal cancers.The MSH3 2436-13g>T mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: No results found
Database Previews
OncoKB
JAX-CKB
Click on previews to view full database entries. External databases may require institutional access.
Computational Analysis
Pathogenicity Predictions
SpliceAIPredictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied
SpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.02 | 48 bp |
| Donor Loss (DL) | 0.0 | -108 bp |
| Acceptor Gain (AG) | 0.01 | 13 bp |
| Donor Gain (DG) | 0.0 | -90 bp |
High impact (≥0.5)
Medium impact (0.2-0.49)
Low impact (<0.2)
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific)
Filter Criteria:
PM2
PM2 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP4
BP4 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP6
BP6 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)