CD177 p.Ile62Phe
c.184A>T · rs1378961137 · VCV3140347
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0498%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.049 | GERP 0.31 |
| Regional constraint | o/e 1.18 | unconstrained · MANE · 8,602 bp · p 3.2e-05 · regional, not allelic |
| Overall | ||
| CADD | 17.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0498%
Middle Eastern · 3/6,022 alleles
Filtering AF
0.0135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00723%
Overall
0.000558%
9/1,613,716 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0498% | 2,007 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| Admixed American | 0.00167% | 60,002 |
| European (non-Finnish) | 0.00017% | 589,887 |
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
- CD177
- Protein
- p.Ile62Phe
- Coding
- c.184A>T
- MANE Select
- NM_020406
- dbSNP
- rs1378961137
- Type
- single nucleotide variant
- Location
- chr19:43353984 (GRCh38)
- Gene constraint
- LOEUF 1.557 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.67 · 2 PDB
Similar variants
- CD177 p.Gly431Arg Benign ★★ same type
- CD177 p.Lys366Arg Benign ★★ same type
- CD177 p.Phe208Val Benign ★★ same type
- CD177 p.Ser364Thr Benign ★★ same type
- CD177 p.Thr210Ile Benign/Likely benign ★★ same type
- CD177 p.Ala281Asp Uncertain significance ★ same type
- CD177 p.Ala3Val Uncertain significance ★ same type
- CD177 p.Ala425Pro Uncertain significance ★ 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/cd177-p-ile62phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown