PGD p.Tyr274=
c.822C>T · rs200238924 · VCV3211785
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -2.5 | GERP -1.9 |
| Overall | ||
| CADD | 7.232 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00136%
22/1,614,030 alleles · ultra-rare
exomes 16/1,461,676 · genomes 6/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| East Asian | 0.0134% | 7,481 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
| Admixed American | 0.00333% | 30,011 |
| African / African-American | 0.00133% | 75,058 |
| European (non-Finnish) | 0.000593% | 168,557 |
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
- PGD
- Protein
- p.Tyr274=
- Coding
- c.822C>T
- MANE Select
- NM_002631
- dbSNP
- rs200238924
- Type
- single nucleotide variant
- Location
- chr1:10413229 (GRCh38)
- Gene constraint
- LOEUF 0.552 · pLI 0.84 (gnomAD)
- Structure
- AlphaFold pLDDT 96.98 · 4 PDB
- Residue 274
- an α-helix
Similar variants
- PGD c.519+2C>T Uncertain significance ★ same type
- PGD p.Ala149Gly Uncertain significance ★ ⚠ same type
- PGD p.Ala258Val Uncertain significance ★ ⚠ same type
- PGD p.Ala336Pro Uncertain significance ★ ⚠ same type
- PGD p.Ala345Gly Uncertain significance ★ ⚠ same type
- PGD p.Arg407Gln Uncertain significance ★ ⚠ same type
- PGD p.Asn354Ser Uncertain significance ★ ⚠ same type
- PGD p.Asn354Tyr 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/pgd-p-tyr274 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown