CITED2 p.Asn9=
c.27C>T · rs200185922 · VCV746097
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0183%, 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 9.8 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 12.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0183%
Admixed American · 11/60,004 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00785%
Overall
0.00606%
97/1,599,558 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0183% | 5,455 |
| European (non-Finnish) | 0.00644% | 15,525 |
| African / African-American | 0.00533% | 18,757 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,795 |
| East Asian | 0.00446% | 22,428 |
| Finnishnot grpmax-eligible | 0.00199% | 50,172 |
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.Asn9=
- Coding
- c.27C>T
- MANE Select
- NM_006079
- dbSNP
- rs200185922
- Type
- single nucleotide variant
- Location
- chr6:139373918 (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.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-asn9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown