EMILIN2 p.Pro854=
c.2562C>G · rs554651277 · VCV777264
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.44%, 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 -4.3 | |
| Overall | ||
| CADD | 0.173 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.44%
African / African-American · 2,288/66,492 alleles
Filtering AF
3.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.28%
Overall
0.196%
2,702/1,376,080 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.44% | 29 |
| Remaining individualsnot grpmax-eligible | 0.288% | 347 |
| Admixed American | 0.244% | 409 |
| Middle Eastern | 0.241% | 416 |
| South Asian | 0.02% | 5,000 |
| European (non-Finnish) | 0.0149% | 6,730 |
| East Asian | 0.00311% | 32,188 |
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
- EMILIN2
- Protein
- p.Pro854=
- Coding
- c.2562C>G
- MANE Select
- NM_032048
- dbSNP
- rs554651277
- Type
- single nucleotide variant
- Location
- chr18:2906985 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.88
- Residue 854
- the collagen-like domain; the 'disordered' region
Similar variants
- EMILIN2 p.Ala215Thr Benign ★★ same type
- EMILIN2 p.Ala455= Benign ★★ same type
- EMILIN2 p.Cys1002= Benign ★★ same type
- EMILIN2 p.Gly843= Benign/Likely benign ★★ same type
- EMILIN2 p.Lys347= Benign ★★ same type
- EMILIN2 p.Met259Val Benign ★★ same type
- EMILIN2 p.Pro136Ser Benign ★★ same type
- EMILIN2 p.Pro657= Benign ★★ 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/emilin2-p-pro854 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown