Genetic Information

Gene & Transcript Details

Gene
CTNNB1
Transcript
NM_001904.4 MANE Select
Total Exons
—
Reference Sequence
NC_000003.11
Alternative Transcripts
IDStatusDetails
NM_001904.3 Alternative 3720 nt | 269–2614
NM_001904.4 MANE Select 3661 nt | 215–2560

Variant Details

HGVS Notation
NM_001904.4:c.1648C>T
Protein Change
R550C
Location
Exon 10 (Exon 10 of )
10
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.0 in 100,000
Extremely Rare
ACMG Criteria Applied PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).

ClinVar

Open
Classification
Uncertain Significance (VUS)
1 publications
Clinical Statement

"This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratories)."

COSMIC Somatic Evidence

Open
COSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
COSMIC 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 CTNNB1.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: CTNNB1R550CCTNNB1R550CSomaticNCBI Gene:1499|Show additional gene information Variant OverviewCTNNB1 (β-catenin), a transcriptional activator, is recurrently mutated in various cancers including endometrial and hepatocellular cancers.The CTNNB1 R550C 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
OncoKB Preview
JAX-CKB
JAX-CKB Preview

Click on previews to view full database entries. External databases may require institutional access.

Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor 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) 0.01 -57 bp
- Donor Loss (DL) 0.01 39 bp
+ Acceptor Gain (AG) 0.0 -143 bp
+ Donor Gain (DG) 0.05 0 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)