EVC p.Arg989del
c.2964AAG[1] · rs777071486 · VCV2037294
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0695%, afr)
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 | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 9.515 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0695%
African / African-American · 52/74,862 alleles
Filtering AF
0.0544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.049%
Overall
0.00397%
64/1,612,292 alleles · ultra-rare
exomes 32/1,460,094 · genomes 32/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0695% | 1,440 |
| Admixed American | 0.01% | 9,993 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,481 |
| South Asian | 0.0011% | 90,632 |
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
- EVC
- Protein
- p.Arg989del
- Coding
- c.2964AAG[1]
- MANE Select
- NM_153717
- dbSNP
- rs777071486
- Type
- Microsatellite
- Location
- chr4:5811020 (GRCh38)
- Gene constraint
- LOEUF 1.134 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.49
- Residue 989
- the 'disordered' region
Similar variants
- EVC p.Arg13fs Pathogenic ★★ same condition
- EVC p.Cys554_Asp555delinsTer Pathogenic/Likely pathogenic ★★ same condition
- EVC p.Leu346fs Pathogenic ★★ same condition
- EVC p.Lys302del Pathogenic/Likely pathogenic ★★ same condition
- EVC p.Phe583fs Pathogenic/Likely pathogenic ★★ same condition
- EVC p.39GL[4] Uncertain significance ★★ same condition
- EVC c.2895-10_2895-9del Benign/Likely benign ★★ same condition
- EVC p.Arg471fs 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/evc-p-arg989del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown