SEC63 p.Asp701=
c.2103C>T · rs747733830 · VCV3058489
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
SEC63-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.78 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 6.586 | 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.Asp701=
- Coding
- c.2103C>T
- MANE Select
- NM_007214
- dbSNP
- rs747733830
- Type
- single nucleotide variant
- Location
- chr6:107872844 (GRCh38)
- Gene constraint
- LOEUF 0.532 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71
- Residue 701
- the sec63 2 domain; a UniProt-annotated variant site (in pcld2)
Disease context
SEC63-related disorder
Similar variants
- SEC63 p.Arg239Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 p.Ser632Ter Pathogenic/Likely pathogenic ★★ same condition
- SEC63 c.224+1G>C Likely pathogenic ★ same condition
- SEC63 c.829-2A>G Likely pathogenic ★ same condition
- SEC63 p.Arg45Ter Pathogenic ★ same condition
- SEC63 p.Tyr33Ter Likely pathogenic ★ same condition
- SEC63 p.His669fs Pathogenic/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-asp701 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown