Genetic Information

Gene & Transcript Details

Gene
SPG11
Transcript
NM_025137.4 MANE Select
Total Exons
—
Reference Sequence
NC_000015.9
Alternative Transcripts
IDStatusDetails
NM_025137.3 Alternative 7817 nt | 32–7363
NM_025137.4 MANE Select 7772 nt | 16–7347
NM_025137.2 Alternative 7752 nt | 2–7333

Variant Details

HGVS Notation
NM_025137.4:c.6062G>A
Protein Change
R2021Q
Location
Exon 32 (Exon 32 of )
32
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.00884 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)
2 publications
Clinical Statement

"This variant has been reported in ClinVar as Likely benign (1 clinical laboratories) and 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 SPG11.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: We do not have any information for this gene 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 33 bp
- Donor Loss (DL) 0.02 -106 bp
+ Acceptor Gain (AG) 0.0 -20 bp
+ Donor Gain (DG) 0.0 -472 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)