SEC63 p.Phe200fs
c.599_600del · VCV3382138
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
polycystic liver disease 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 21 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SEC63
- Protein
- p.Phe200fs
- Coding
- c.599_600del
- MANE Select
- NM_007214
- Type
- Deletion
- Location
- chr6:107911370 (GRCh38)
- Gene constraint
- LOEUF 0.532 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71
- Residue 200
- a UniProt-annotated variant site (in pcld2); the sec63 1 domain
Similar variants
- SEC63 p.His669fs Pathogenic/Likely pathogenic ★★ same condition
- SEC63 c.125-13del Likely benign ★★ same condition
- SEC63 c.1936-11_1936-9del Benign/Likely benign ★★ same condition
- SEC63 c.1936-9del Benign/Likely benign ★★ same condition
- SEC63 c.340-12_340-11del Benign/Likely benign ★★ same condition
- SEC63 c.340-12_340-8del Benign/Likely benign ★★ same condition
- SEC63 c.340-9_340-7del Benign/Likely benign ★★ same condition
- SEC63 c.506_514+3del Likely pathogenic ★ same condition
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/sec63-p-phe200fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown