SEC23B p.Pro636=
c.1908A>G · VCV4944520
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.53e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.38 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.7 | GERP -5.7 |
| Overall | ||
| CADD | 0.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.53e-05%
European (non-Finnish) · 1/1,172,488 alleles
Overall
6.25e-05%
1/1,600,164 alleles · very rare
exomes 1/1,447,856 · genomes 0/152,308 · joint denominator
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
- SEC23B
- Protein
- p.Pro636=
- Coding
- c.1908A>G
- MANE Select
- NM_006363
- Type
- single nucleotide variant
- Location
- chr20:18551091 (GRCh38)
- Gene constraint
- LOEUF 1.008 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.41
- Residue 636
- a UniProt-annotated variant site (in cdan2)
Similar variants
- SEC23B c.1314+1G>A Likely pathogenic ★★ same type
- SEC23B c.835-2A>G Pathogenic/Likely pathogenic ★★ same type
- SEC23B p.Ala524Val Pathogenic/Likely pathogenic ★★ same type
- SEC23B p.Arg14Trp Pathogenic/Likely pathogenic ★★ same type
- SEC23B p.Arg264Ter Pathogenic ★★ same type
- SEC23B p.Arg313His Pathogenic/Likely pathogenic ★★ same type
- SEC23B p.Arg324Ter Pathogenic/Likely pathogenic ★★ same type
- SEC23B p.Arg339Ter 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/sec23b-p-pro636 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown