Genetic Information

Gene & Transcript Details

Gene
PALB2
Transcript
NM_024675.4 MANE Select
Total Exons
—
Reference Sequence
NC_000016.9
Alternative Transcripts
IDStatusDetails
NM_024675.4 MANE Select 4008 nt | 154–3714
NM_024675.3 RefSeq Select 4069 nt | 201–3761

Variant Details

HGVS Notation
NM_024675.4:c.1058A>T
Protein Change
K353I
Location
Exon 4 (Exon 4 of )
4
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 PALB2.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: PALB2K353IPALB2K353ISomaticNCBI Gene:79728|Show additional gene information Variant OverviewPALB2, a scaffolding protein involved in DNA repair, is altered in various cancers.The PALB2 K353I mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: PALB2 K353Ifs*7 indicates a shift in the reading frame starting at amino acid 353 and terminating seven residues downstream causing a premature truncation of the 1186 amino acid Palb2 protein (UniProt.org). K353Ifs*7 has not been characterized, however, due to the effects of other truncation mutations downstream of K353 (PMID: 31636395, PMID: 31757951), is predicted to lead to a loss of Palb2 protein function.

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 -162 bp
- Donor Loss (DL) 0.0 -56 bp
+ Acceptor Gain (AG) 0.0 -117 bp
+ Donor Gain (DG) 0.0 364 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)