ERC1 p.Ser509=
c.1527C>T · rs138901829 · VCV3051178
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.87%, eas)
Conditions
1
ERC1-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 -1.1 | GERP -0.72 |
| Overall | ||
| CADD | 9.475 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.87%
East Asian · 841/44,876 alleles
Filtering AF
1.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.73%
Overall
0.0586%
946/1,613,956 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.87% | 53 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| South Asian | 0.0264% | 3,793 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.004% | 25,009 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,586 |
| Finnishnot grpmax-eligible | 0.00312% | 32,016 |
| European (non-Finnish) | 0.00263% | 38,062 |
| Admixed American | 0.00167% | 59,998 |
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.Ser509=
- Coding
- c.1527C>T
- MANE Select
- NM_178040
- dbSNP
- rs138901829
- Type
- single nucleotide variant
- Location
- chr12:1115991 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.79 (gnomAD)
- Structure
- AlphaFold pLDDT 75.64
Disease context
ERC1-related disorder
Similar variants
- ERC1 c.1738-6A>C Likely benign same condition
- ERC1 c.2158-4G>A Benign same condition
- ERC1 c.3214-9201G>T Likely benign same condition
- ERC1 c.3214-9246C>T Benign same condition
- ERC1 p.Ala940= Benign same condition
- ERC1 p.Arg103Pro Likely benign ⚠ same condition
- ERC1 p.Gln16His Benign same condition
- ERC1 p.His342= Likely benign 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/erc1-p-ser509 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown