CEP120 p.Ala790=
c.2370T>C · VCV4714743
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00114%, sas)
Conditions
1
short-rib thoracic dysplasia 13 with or without polydactyly
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 2.9 | phastCons 1 |
| Overall | ||
| CADD | 12.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00114%
South Asian · 1/87,934 alleles
Overall
0.000138%
2/1,445,706 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00114% | 87,934 |
| European (non-Finnish) | 8.53e-05% | 1,172,986 |
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
- CEP120
- Protein
- p.Ala790=
- Coding
- c.2370T>C
- MANE Select
- NM_001375405
- Type
- single nucleotide variant
- Location
- chr5:123372761 (GRCh38)
- Gene constraint
- LOEUF 0.93 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.22 · 4 PDB
Similar variants
- CEP120 c.1255+1G>A Likely pathogenic ★★ same condition
- CEP120 c.2580+2T>A Likely pathogenic ★★ same condition
- CEP120 p.Ala199Pro Pathogenic/Likely pathogenic ★★ same condition
- CEP120 p.Arg722Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP120 p.Gln775Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP120 p.Lys539Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP120 c.1038+6T>C Uncertain significance ★★ same condition
- CEP120 c.2481+6C>T Uncertain significance ★★ same condition
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/cep120-p-ala790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown