IL10 p.Phe164Ser
c.491T>C · VCV4678391
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9788 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9788 | likely pathogenic · top 3% in IL10 |
|---|---|---|
| REVEL | 0.786 | moderately pathogenic-leaning |
| SaProt | LLR -7.89 | tolerated |
| ⇒ AlphaMissense and REVEL call this damaging; SaProt does not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.5, phastCons 1 |
| Regional constraint | o/e 0.76 | unconstrained · MANE · 3,796 bp · p 0.00037 · regional, not allelic |
| Overall | ||
| CADD | 28.7 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- IL10
- Protein
- p.Phe164Ser
- Coding
- c.491T>C
- MANE Select
- NM_000572
- Type
- single nucleotide variant
- Location
- chr1:206768682 (GRCh38)
- Gene constraint
- LOEUF 0.711 · pLI 0.48 (gnomAD)
- Structure
- AlphaFold pLDDT 88.89 · 9 PDB
- Residue 164
- an α-helix
Similar variants
- IL10 p.Phe164= Likely benign ★ same residue
- IL10 c.225+6A>G Uncertain significance ★★ same type
- IL10 p.Arg124Trp Uncertain significance ★★ ⚠ same type
- IL10 p.Arg177Ter Uncertain significance ★★ same type
- IL10 p.Glu169Asp Uncertain significance ★★ ⚠ same type
- IL10 p.Leu13Met Uncertain significance ★★ ⚠ same type
- IL10 c.165+20G>A Likely benign ★★ same type
- IL10 c.165+8T>C 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/il10-p-phe164ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown