SEC63 p.Thr463=
c.1389A>G · rs2482042579 · VCV3064701
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
polycystic liver disease 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.27 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.93 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 15.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SEC63
- Protein
- p.Thr463=
- Coding
- c.1389A>G
- MANE Select
- NM_007214
- dbSNP
- rs2482042579
- Type
- single nucleotide variant
- Location
- chr6:107897700 (GRCh38)
- Gene constraint
- LOEUF 0.532 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71
- Residue 463
- a UniProt-annotated variant site (in pcld2); the sec63 1 domain
Similar variants
- SEC63 c.452+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SEC63 c.625-2A>G Likely pathogenic ★★ same condition
- SEC63 c.733+1G>A Pathogenic ★★ same condition
- SEC63 p.Arg239Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 p.Arg622Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 p.Ser632Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 c.452+3A>G Uncertain significance ★★ 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-thr463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown