PHF2 p.Ser725=
c.2175G>A · rs34289742 · VCV781169
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.89%, 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 -8.7 | GERP -2.8 |
| Overall | ||
| CADD | 0.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.89%
African / African-American · 1,418/75,014 alleles
Filtering AF
1.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.78%
Overall
0.105%
1,688/1,613,092 alleles · low-frequency
exomes 841/1,460,870 · genomes 847/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.89% | 53 |
| Admixed American | 0.13% | 770 |
| Remaining individualsnot grpmax-eligible | 0.125% | 801 |
| Middle Eastern | 0.0495% | 2,019 |
| Finnishnot grpmax-eligible | 0.00945% | 10,584 |
| European (non-Finnish) | 0.00848% | 11,796 |
| South Asian | 0.00549% | 18,212 |
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
- PHF2
- Protein
- p.Ser725=
- Coding
- c.2175G>A
- MANE Select
- NM_005392
- dbSNP
- rs34289742
- Type
- single nucleotide variant
- Location
- chr9:93666048 (GRCh38)
- Gene constraint
- LOEUF 0.329 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.14 · 9 PDB
- Residue 725
- the 'disordered' region
Similar variants
- PHF2 p.Ser725Leu Likely benign same residue
- PHF2 c.299+7T>A Benign ★★ same type
- PHF2 c.789+10G>A Benign/Likely benign ★★ same type
- PHF2 p.Asp103= Benign ★★ same type
- PHF2 p.Leu645= Benign/Likely benign ★★ same type
- PHF2 p.Pro786= Benign ★★ same type
- PHF2 p.Pro988= Benign ★★ same type
- PHF2 p.Ser738= 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/phf2-p-ser725 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown