SERAC1 p.Asp62=
c.186T>C · rs2483596755 · VCV3046880
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
SERAC1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 7.599 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,766 alleles
Overall
0.000125%
2/1,597,986 alleles · very rare
exomes 2/1,445,688 · genomes 0/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,766 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 61,986 |
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
- SERAC1
- Protein
- p.Asp62=
- Coding
- c.186T>C
- MANE Select
- NM_032861
- dbSNP
- rs2483596755
- Type
- single nucleotide variant
- Location
- chr6:158150532 (GRCh38)
- Gene constraint
- LOEUF 0.681 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.66
Disease context
SERAC1-related disorder
Similar variants
- SERAC1 c.1403+1G>C Pathogenic ★★ same condition
- SERAC1 p.Ser498Thr Pathogenic/Likely pathogenic ★★ same condition
- SERAC1 c.91+1G>C Likely pathogenic ★ same condition
- SERAC1 c.1308+8A>G Likely benign same condition
- SERAC1 c.92-245G>A Likely benign same condition
- SERAC1 p.Asn522= Likely benign same condition
- SERAC1 c.1822_1828+10delinsACCAACAGG Pathogenic/Likely pathogenic ★★ same condition
- SERAC1 p.Ala609fs 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/serac1-p-asp62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown