Genetic Information

Gene & Transcript Details

Gene
CUX1
Transcript
NM_001202543.1 MANE Select
Total Exons
—
Reference Sequence
NC_000007.13
Alternative Transcripts
IDStatusDetails
NM_001202543.1 Alternative 13882 nt | 128–4678
NM_001202543.2 Alternative 13766 nt | 25–4575

Variant Details

HGVS Notation
NM_001202543.1:c.1227G>A
Protein Change
A409=
Location
Exon 14 (Exon 14 of )
14
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.000817 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
Unknown
0 publications
Clinical Statement

""

COSMIC Somatic Evidence

Open
COSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not Applied
COSMIC Database Preview
COSMIC Preview
Accessing full COSMIC database details requires institutional login or subscription.

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 CUX1.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: CUX1A409=CUX1A409=SomaticNCBI Gene:1523|Show additional gene information Variant OverviewCUX1, a transcription factor, is frequently altered in several cancers types by deletion, mutation or translocation.This is a synonymous mutation and is not annotated by OncoKB. 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) 0.0 -94 bp
- Donor Loss (DL) 0.0 263 bp
+ Acceptor Gain (AG) 0.0 224 bp
+ Donor Gain (DG) 0.0 32 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)