PHF13 p.Ser177=
c.531G>A · rs116799550 · VCV716040
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.23%, afr)
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 -8.6 | GERP -3.4 |
| Overall | ||
| CADD | 0.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.23%
African / African-American · 1,672/75,014 alleles
Filtering AF
2.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.1%
Overall
0.144%
2,328/1,613,932 alleles · low-frequency
exomes 1,240/1,461,752 · genomes 1,088/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.23% | 45 |
| Admixed American | 0.315% | 317 |
| Remaining individualsnot grpmax-eligible | 0.19% | 525 |
| Middle Eastern | 0.148% | 674 |
| European (non-Finnish) | 0.0282% | 3,544 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,869 |
| South Asian | 0.00329% | 30,361 |
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
- PHF13
- Protein
- p.Ser177=
- Coding
- c.531G>A
- MANE Select
- NM_153812
- dbSNP
- rs116799550
- Type
- single nucleotide variant
- Location
- chr1:6620192 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.80 · 2 PDB
- Residue 177
- the 'disordered' region
Similar variants
- PHF13 c.141+10T>C Benign ★★ same type
- PHF13 p.Ala78Thr Uncertain significance ★ ⚠ same type
- PHF13 p.Arg88Cys Uncertain significance ★ ⚠ same type
- PHF13 p.Asn250Ser Uncertain significance ★ ⚠ same type
- PHF13 p.Asn29Lys Uncertain significance ★ ⚠ same type
- PHF13 p.Glu47Lys Uncertain significance ★ ⚠ same type
- PHF13 p.Gly131Ala Uncertain significance ★ ⚠ same type
- PHF13 p.Gly134Arg 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/phf13-p-ser177 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown