EGFL6 p.Phe20=
c.60C>T · rs1467117510 · VCV2660024
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0123%, sas)
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 0.39 | GERP -0.83, phastCons 0.11 |
| Overall | ||
| CADD | 7.846 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0123%
South Asian · 7/56,856 alleles
Filtering AF
0.0057%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00408%
Overall
0.000578%
7/1,210,303 alleles · ultra-rare
exomes 6/1,097,705 · genomes 1/112,598 · joint denominator
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
- EGFL6
- Protein
- p.Phe20=
- Coding
- c.60C>T
- MANE Select
- NM_015507
- dbSNP
- rs1467117510
- Type
- single nucleotide variant
- Location
- chrX:13569921 (GRCh38)
- Structure
- AlphaFold pLDDT 65.96
Similar variants
- EGFL6 p.Arg448Gln Uncertain significance ★★ ⚠ same type
- EGFL6 p.Arg103Trp Likely benign ★★ ⚠ same type
- EGFL6 p.Arg108= Benign ★★ same type
- EGFL6 p.Arg164Cys Benign ★★ ⚠ same type
- EGFL6 p.Glu66Lys Benign ★★ same type
- EGFL6 p.Leu508Phe Benign ★★ same type
- EGFL6 p.Lys117= Benign ★★ same type
- EGFL6 p.Tyr116= 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/egfl6-p-phe20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown