CNGA1 p.Lys519fs
c.1557del · rs2110128153 · VCV1075000
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 6.2 | GERP 3.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CNGA1
- Protein
- p.Lys519fs
- Coding
- c.1557del
- MANE Select
- NM_001379270
- dbSNP
- rs2110128153
- Type
- Deletion
- Location
- chr4:47936925 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.88 · 19 PDB
- Residue 519
- the 'cyclic nucleotide-binding domain' region
Similar variants
- CNGA1 p.Lys519Arg Uncertain significance ★★ same residue
- CNGA1 p.Asn175_Trp176insTer Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Asn334_Asp335insTer Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Asp575fs Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Gly60fs Pathogenic ★★ same type
- CNGA1 p.Leu85fs Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Lys414fs Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Thr177fs 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/cnga1-p-lys519fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown