SEC63 p.Phe16del
c.44TCT[1] · rs752984272 · VCV3065873
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
polycystic liver disease 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 1.5, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,842 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000744%
12/1,613,258 alleles · very rare
exomes 12/1,461,222 · genomes 0/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,842 |
| African / African-American | 0.00133% | 74,924 |
| South Asian | 0.0011% | 91,066 |
| European (non-Finnish) | 0.000763% | 131,057 |
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.Phe16del
- Coding
- c.44TCT[1]
- MANE Select
- NM_007214
- dbSNP
- rs752984272
- Type
- Microsatellite
- Location
- chr6:107957961 (GRCh38)
- Gene constraint
- LOEUF 0.532 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71
- Residue 16
- a UniProt-annotated variant site (in pcld2)
Similar variants
- SEC63 p.Asp596fs Likely pathogenic ★★ same condition
- SEC63 c.125_126del Likely pathogenic ★ same condition
- SEC63 p.Tyr444fs Pathogenic ★ same condition
- SEC63 p.Glu568del Conflicting classifications of pathogenicity ★ same condition
- SEC63 p.Glu580del Uncertain significance ★ same condition
- 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
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-phe16del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown