SEC24D p.Pro85fs
c.252del · VCV3661126
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -3.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SEC24D
- Protein
- p.Pro85fs
- Coding
- c.252del
- MANE Select
- NM_014822
- Type
- Deletion
- Location
- chr4:118817409 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.21 · 6 PDB
- Residue 85
- the 'disordered' region
Similar variants
- SEC24D p.Val90fs Pathogenic/Likely pathogenic ★★ same type
- SEC24D c.1708-4_1708-3del Benign/Likely benign ★★ same type
- SEC24D p.Gln4fs Likely pathogenic ★ same type
- SEC24D p.Gln533fs Pathogenic ★ same type
- SEC24D p.Leu737fs Pathogenic ★ same type
- SEC24D p.Lys660_Asn662del Likely pathogenic ★ same type
- SEC24D p.Thr702fs Likely pathogenic ★ same type
- SEC24D c.1296+4del Uncertain significance ★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/sec24d-p-pro85fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown