CEP250 p.Ala1973=
c.5919T>A · rs752488973 · VCV2427982
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00146%, nfe)
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 -0.014 | GERP -2.4, phastCons 0.86 |
| Overall | ||
| CADD | 3.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00146%
European (non-Finnish) · 17/1,167,948 alleles
Filtering AF
0.000887%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000725%
Overall
0.00113%
18/1,588,496 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00146% | 68,703 |
| African / African-American | 0.00135% | 74,306 |
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
- CEP250
- Protein
- p.Ala1973=
- Coding
- c.5919T>A
- MANE Select
- NM_007186
- dbSNP
- rs752488973
- Type
- single nucleotide variant
- Location
- chr20:35504288 (GRCh38)
- Gene constraint
- LOEUF 0.86 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 1 PDB
- Residue 1973
- a UniProt-annotated variant site (in crdhl2); a UniProt-annotated variant site (in crdhl2; also found in a family with non-syndromic retinitis pigmentosa); a UniProt-annotated variant site (in crdhl2; the retinal involvement is more severe in double homozygotes also carrying a pcare truncating variant)
Similar variants
- CEP250 p.Ala1973Val Uncertain significance ★ ⚠ same residue
- CEP250 p.Arg1045Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1155Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1336Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1343Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1499Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1695Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1869Ter Pathogenic/Likely pathogenic ★★ 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/cep250-p-ala1973 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown