CITED2 p.Ser170=
c.510G>C · rs139128813 · VCV776166
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.36%, afr)
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 0.63 | GERP -1.4, phastCons 0.84 |
| Overall | ||
| CADD | 7.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.36%
African / African-American · 1,665/70,612 alleles
Filtering AF
2.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.23%
Overall
0.127%
1,937/1,519,228 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.36% | 42 |
| Admixed American | 0.174% | 576 |
| Remaining individualsnot grpmax-eligible | 0.166% | 601 |
| Middle Eastern | 0.142% | 704 |
| European (non-Finnish) | 0.00712% | 14,048 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00409% | 24,430 |
| South Asian | 0.00399% | 25,039 |
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.Ser170=
- Coding
- c.510G>C
- MANE Select
- NM_006079
- dbSNP
- rs139128813
- Type
- single nucleotide variant
- Location
- chr6:139373435 (GRCh38)
- Gene constraint
- LOEUF 0.588 · pLI 0.90 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.07 · 4 PDB
- Residue 170
- the 'disordered' region; a UniProt-annotated variant site (in vsd2; reduces coactivation of the tfap2c gene to 50% of that obtained with wild-type and represses hif1a with about 60% efficiency compared to wild-type)
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-ser170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown