YY1AP1 p.Pro673=
c.2019C>G · VCV3910123
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0482%, nfe)
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 1.1 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 7.076 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0482%
European (non-Finnish) · 569/1,180,032 alleles
Filtering AF
0.0449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0436%
Overall
0.0385%
622/1,614,172 alleles · ultra-rare
exomes 577/1,461,876 · genomes 45/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0482% | 2,074 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,808 |
| South Asian | 0.0187% | 5,358 |
| Middle Eastern | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.0141% | 7,114 |
| African / African-American | 0.00933% | 10,718 |
| East Asian | 0.00891% | 11,223 |
| Admixed American | 0.00333% | 30,009 |
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.Pro673=
- Coding
- c.2019C>G
- MANE Select
- NM_139119
- Type
- single nucleotide variant
- Location
- chr1:155659891 (GRCh38)
- Gene constraint
- LOEUF 1.319 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.58
- Residue 673
- a UniProt-annotated variant site (in grng)
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-pro673 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown