EMILIN1 p.Pro52=
c.156A>G · rs750223152 · VCV2650757
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0581%, eas)
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 -2 | GERP -3.5 |
| Overall | ||
| CADD | 2.177 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0581%
East Asian · 24/41,318 alleles
Filtering AF
0.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.034%
Overall
0.00159%
25/1,571,362 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0581% | 1,722 |
| European (non-Finnish) | 8.59e-05% | 1,164,768 |
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
- EMILIN1
- Protein
- p.Pro52=
- Coding
- c.156A>G
- MANE Select
- NM_007046
- dbSNP
- rs750223152
- Type
- single nucleotide variant
- Location
- chr2:27079221 (GRCh38)
- Gene constraint
- LOEUF 0.832 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.73 · 2 PDB
Similar variants
- EMILIN1 p.Pro52Thr Uncertain significance ★ ⚠ same residue
- EMILIN1 p.Arg107His Uncertain significance ★★ ⚠ same type
- EMILIN1 p.Arg594His Uncertain significance ★★ ⚠ same type
- EMILIN1 p.Gly374Ser Uncertain significance ★★ ⚠ same type
- EMILIN1 p.His805Arg Uncertain significance ★★ ⚠ same type
- EMILIN1 c.2576-8C>A Likely benign ★★ same type
- EMILIN1 p.Gln536Arg Benign ★★ same type
- EMILIN1 p.Gly672= Benign/Likely 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/emilin1-p-pro52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown