SEC63 p.Glu457=
c.1371A>G · rs558158310 · VCV3040323
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.238%, sas)
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 1.6 | GERP 0.57, phastCons 1 |
| Overall | ||
| CADD | 8.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.238%
South Asian · 216/90,900 alleles
Filtering AF
0.212%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.202%
Overall
0.0146%
234/1,606,110 alleles · rare
exomes 224/1,453,818 · genomes 10/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.238% | 421 |
| Remaining individualsnot grpmax-eligible | 0.0145% | 6,917 |
| Admixed American | 0.00167% | 60,026 |
| European (non-Finnish) | 0.000682% | 146,614 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SEC63
- Protein
- p.Glu457=
- Coding
- c.1371A>G
- MANE Select
- NM_007214
- dbSNP
- rs558158310
- Type
- single nucleotide variant
- Location
- chr6:107897718 (GRCh38)
- Gene constraint
- LOEUF 0.532 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71
- Residue 457
- a UniProt-annotated variant site (in pcld2); the sec63 1 domain
Similar variants
- SEC63 c.452+1G>A Pathogenic/Likely pathogenic ★★ same type
- SEC63 c.625-2A>G Likely pathogenic ★★ same type
- SEC63 c.733+1G>A Pathogenic ★★ same type
- SEC63 p.Arg239Ter Pathogenic/Likely pathogenic ★★ same type
- SEC63 p.Arg622Ter Pathogenic/Likely pathogenic ★★ same type
- SEC63 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same type
- SEC63 p.Ser632Ter Pathogenic/Likely pathogenic ★★ same type
- SEC63 p.Trp58Ter Pathogenic ★★ 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/sec63-p-glu457 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown