PHF2 p.Pro988=
c.2964G>T · rs10992855 · VCV722562
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.68%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -3.2, phastCons 0.026 |
| Overall | ||
| CADD | 0.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.68%
African / African-American · 670/11,788 alleles
Filtering AF
5.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.19%
Overall
0.326%
1,440/441,432 alleles · common
exomes 1,007/416,234 · genomes 433/25,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.68% | 18 |
| Middle Eastern | 0.465% | 215 |
| Admixed American | 0.406% | 247 |
| Finnishnot grpmax-eligible | 0.335% | 298 |
| Remaining individualsnot grpmax-eligible | 0.33% | 303 |
| European (non-Finnish) | 0.176% | 567 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0561% | 1,783 |
| South Asian | 0.0546% | 1,832 |
| East Asian | 0.0472% | 2,121 |
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.Pro988=
- Coding
- c.2964G>T
- MANE Select
- NM_005392
- dbSNP
- rs10992855
- Type
- single nucleotide variant
- Location
- chr9:93676725 (GRCh38)
- Gene constraint
- LOEUF 0.329 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.14 · 9 PDB
- Residue 988
- the 'disordered' region
Similar variants
- PHF2 p.Pro988Leu Uncertain significance ★ ⚠ 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.Ser725= 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-pro988 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown