CITED2 p.Pro167=
c.501C>T · rs765262697 · VCV3025178
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0146%, eas)
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 0.066 | GERP -3.5, phastCons 0.64 |
| Overall | ||
| CADD | 9.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0146%
East Asian · 6/41,132 alleles
Filtering AF
0.00632%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00433%
Overall
0.000782%
12/1,534,256 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0146% | 6,855 |
| South Asian | 0.00517% | 19,339 |
| Admixed American | 0.002% | 49,918 |
| Remaining individualsnot grpmax-eligible | 0.0017% | 58,990 |
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.Pro167=
- Coding
- c.501C>T
- MANE Select
- NM_006079
- dbSNP
- rs765262697
- Type
- single nucleotide variant
- Location
- chr6:139373444 (GRCh38)
- Gene constraint
- LOEUF 0.588 · pLI 0.90 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.07 · 4 PDB
- Residue 167
- the 'disordered' region
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.Pro209= 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-pro167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown