EVC2 p.Glu829=
c.2487G>A · rs16837501 · VCV262612
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.18%, eas)
Conditions
2
Ellis-van Creveld syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.27 | GERP 1, phastCons 0.99 |
| Overall | ||
| CADD | 0.989 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.18%
East Asian · 1,425/44,824 alleles
Filtering AF
3.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.99%
Overall
0.16%
2,575/1,613,874 alleles · low-frequency
exomes 2,253/1,461,688 · genomes 322/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.18% | 31 |
| Finnishnot grpmax-eligible | 0.764% | 131 |
| Remaining individualsnot grpmax-eligible | 0.216% | 463 |
| South Asian | 0.156% | 641 |
| Middle Eastern | 0.066% | 1,515 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0541% | 1,850 |
| European (non-Finnish) | 0.0303% | 3,296 |
| Admixed American | 0.005% | 20,007 |
| African / African-American | 0.004% | 25,004 |
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
- EVC2
- Protein
- p.Glu829=
- Coding
- c.2487G>A
- MANE Select
- NM_147127
- dbSNP
- rs16837501
- Type
- single nucleotide variant
- Location
- chr4:5622551 (GRCh38)
- Gene constraint
- LOEUF 1.092 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 73.33
Similar variants
- EVC2 c.2046+1G>A Likely pathogenic ★★ same condition
- EVC2 c.2047-2A>G Likely pathogenic ★★ same condition
- EVC2 c.229-1G>T Likely pathogenic ★★ same condition
- EVC2 c.229-2A>G Likely pathogenic ★★ same condition
- EVC2 c.3360+1G>A Pathogenic ★★ same condition
- EVC2 c.3659+2T>C Pathogenic/Likely pathogenic ★★ same condition
- EVC2 c.450+2T>C Likely pathogenic ★★ same condition
- EVC2 c.451-2A>G 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/evc2-p-glu829 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown