CITED2 p.Pro209=
c.627C>T · rs767902739 · VCV733119
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.193%, 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 -0.83 | GERP -3.5 |
| Overall | ||
| CADD | 7.403 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.193%
Admixed American · 116/59,988 alleles
Filtering AF
0.165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.154%
Overall
0.00837%
135/1,612,794 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.193% | 517 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,491 |
| African / African-American | 0.00668% | 14,981 |
| European (non-Finnish) | 0.000763% | 131,090 |
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
- CITED2
- Protein
- p.Pro209=
- Coding
- c.627C>T
- MANE Select
- NM_006079
- dbSNP
- rs767902739
- Type
- single nucleotide variant
- Location
- chr6:139373318 (GRCh38)
- Gene constraint
- LOEUF 0.588 · pLI 0.90 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.07 · 4 PDB
Similar variants
- CITED2 p.Ala25Pro Uncertain significance ★★ ⚠ same type
- CITED2 p.Ala25Val Uncertain significance ★★ ⚠ same type
- CITED2 p.Pro128Ser Uncertain significance ★★ ⚠ same type
- CITED2 p.Ala7= Benign ★★ same type
- CITED2 p.Gly194= Benign/Likely benign ★★ same type
- CITED2 p.His160Leu Benign/Likely benign ★★ same type
- CITED2 p.His46= Likely benign ★★ same type
- CITED2 p.Ser192Gly Benign/Likely 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/cited2-p-pro209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown