CEP170B p.Ala259Val
c.776C>T · rs41304371 · VCV781153
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.5%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -1.9 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 19 kb · p 0.99 · regional, not allelic |
| Overall | ||
| CADD | 3.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.5%
African / African-American · 1,862/74,620 alleles
Filtering AF
2.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.36%
Overall
0.21%
3,381/1,611,214 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.5% | 40 |
| Finnishnot grpmax-eligible | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.194% | 516 |
| Admixed American | 0.157% | 637 |
| Middle Eastern | 0.149% | 673 |
| European (non-Finnish) | 0.0897% | 1,115 |
| South Asian | 0.066% | 1,516 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
| East Asian | 0.00223% | 44,814 |
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
- CEP170B
- Protein
- p.Ala259Val
- Coding
- c.776C>T
- MANE Select
- NM_001112726
- dbSNP
- rs41304371
- Type
- single nucleotide variant
- Location
- chr14:104883233 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.31
- Residue 259
- the 'disordered' region
Similar variants
- CEP170B p.Lys368Glu Uncertain significance ★★ same type
- CEP170B p.Pro148Leu Uncertain significance ★★ same type
- CEP170B p.Arg147= Benign ★★ same type
- CEP170B p.Ala1053Val Uncertain significance ★ same type
- CEP170B p.Ala1062Val Uncertain significance ★ same type
- CEP170B p.Ala1083Val Uncertain significance ★ same type
- CEP170B p.Ala1091Thr Uncertain significance ★ same type
- CEP170B p.Ala1123Thr 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/cep170b-p-ala259val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown