Genetic Information

Gene & Transcript Details

Gene
BCORL1
Transcript
NM_021946.4 MANE Select
Total Exons
—
Reference Sequence
NC_000023.10
Alternative Transcripts
IDStatusDetails
NM_021946.5 Alternative 7243 nt | 173–5308
NM_021946.3 Alternative 7252 nt | 170–5305
NM_021946.2 Alternative 6740 nt | 115–5250
NM_021946.4 Alternative 7127 nt | 45–5180

Variant Details

HGVS Notation
NM_021946.4:c.4464C>T
Protein Change
D1488=
Location
Exon 8 (Exon 8 of )
8
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.00396 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
COSM611002
Recurrence
5 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 BCORL1.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: BCORL1D1488=BCORL1D1488=SomaticNCBI Gene:63035|Show additional gene information Variant OverviewBCORL1, a transcriptional repressor, is recurrently mutated in hematopoietic malignancies, astrocytomas, and intracranial germ cell tumors.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) 0.01 -134 bp
- Donor Loss (DL) 0.0 -3 bp
+ Acceptor Gain (AG) 0.0 92 bp
+ Donor Gain (DG) 0.0 -11 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)