YY1AP1 p.Pro128=
c.384G>A · rs367625562 · VCV2752448
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
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 -5.1 | GERP -3.7 |
| Overall | ||
| CADD | 3.824 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/59,968 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00403%
65/1,613,368 alleles · ultra-rare
exomes 58/1,461,332 · genomes 7/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,748 |
| South Asian | 0.00769% | 13,010 |
| European (non-Finnish) | 0.00331% | 30,248 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,227 |
| African / African-American | 0.00134% | 74,816 |
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
- YY1AP1
- Protein
- p.Pro128=
- Coding
- c.384G>A
- MANE Select
- NM_139119
- dbSNP
- rs367625562
- Type
- single nucleotide variant
- Location
- chr1:155675037 (GRCh38)
- Gene constraint
- LOEUF 1.319 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.58
Similar variants
- YY1AP1 c.412-1G>A Pathogenic ★★ same type
- YY1AP1 p.Gln84Ter Pathogenic/Likely pathogenic ★★ same type
- YY1AP1 p.Gln75His Uncertain significance ★★ ⚠ same type
- YY1AP1 p.Ile135Met Uncertain significance ★★ ⚠ same type
- YY1AP1 c.324+7C>T Likely benign ★★ same type
- YY1AP1 p.Ala579= Benign ★★ same type
- YY1AP1 p.Ala591= Likely benign ★★ same type
- YY1AP1 p.Gln435Arg 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/yy1ap1-p-pro128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown