ERC1 p.Ser393=
c.1179T>A · rs36113377 · VCV776684
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.74%, afr)
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 -0.1 | GERP 0.26, phastCons 0.81 |
| Overall | ||
| CADD | 8.561 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.74%
African / African-American · 3,547/74,866 alleles
Filtering AF
4.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.55%
Overall
0.294%
4,737/1,611,352 alleles · low-frequency
exomes 2,654/1,459,048 · genomes 2,083/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.74% | 21 |
| Middle Eastern | 1.23% | 82 |
| Admixed American | 0.531% | 188 |
| Remaining individualsnot grpmax-eligible | 0.463% | 216 |
| European (non-Finnish) | 0.0405% | 2,472 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0339% | 2,952 |
| South Asian | 0.0277% | 3,615 |
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
- ERC1
- Protein
- p.Ser393=
- Coding
- c.1179T>A
- MANE Select
- NM_178040
- dbSNP
- rs36113377
- Type
- single nucleotide variant
- Location
- chr12:1110209 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.79 (gnomAD)
- Structure
- AlphaFold pLDDT 75.64
Similar variants
- ERC1 c.3214-1G>A Uncertain significance ★ same type
- ERC1 p.Ala1058Val Uncertain significance ★ ⚠ same type
- ERC1 p.Ala199Thr Uncertain significance ★ ⚠ same type
- ERC1 p.Ala260Glu Uncertain significance ★ ⚠ same type
- ERC1 p.Ala5Ser Uncertain significance ★ ⚠ same type
- ERC1 p.Ala621Thr Uncertain significance ★ ⚠ same type
- ERC1 p.Ala682Ser Uncertain significance ★ ⚠ same type
- ERC1 p.Ala720Thr Uncertain significance ★ ⚠ 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/erc1-p-ser393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown