CITED1 p.Val162=
c.486G>A · rs145731331 · VCV730182
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.673%, 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 2.6 | GERP 3.8, phastCons 1 |
| Overall | ||
| CADD | 10.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.673%
African / African-American · 385/57,230 alleles
Filtering AF
0.617%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.596%
Overall
0.0356%
431/1,210,312 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.673% | 149 |
| Remaining individualsnot grpmax-eligible | 0.0483% | 2,070 |
| Admixed American | 0.0327% | 3,054 |
| European (non-Finnish) | 0.000894% | 111,914 |
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
- CITED1
- Protein
- p.Val162=
- Coding
- c.486G>A
- MANE Select
- NM_001144887
- dbSNP
- rs145731331
- Type
- single nucleotide variant
- Location
- chrX:72301819 (GRCh38)
- Structure
- AlphaFold pLDDT 60.42
Similar variants
- CITED1 p.Ala118Thr Uncertain significance ★ ⚠ same type
- CITED1 p.Ala130Glu Uncertain significance ★ ⚠ same type
- CITED1 p.Ala187Val Uncertain significance ★ ⚠ same type
- CITED1 p.Asn171Ser Uncertain significance ★ ⚠ same type
- CITED1 p.Asn23His Uncertain significance ★ ⚠ same type
- CITED1 p.Asn53Ser Uncertain significance ★ ⚠ same type
- CITED1 p.Asn53Tyr Uncertain significance ★ ⚠ same type
- CITED1 p.Gly116Arg 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/cited1-p-val162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown