Is CNGA3 p.Phe301Ter (c.902_903delinsAA) pathogenic?

CNGA3 p.Phe301Ter (c.902903delinsAA) is classified Pathogenic/Likely pathogenic in CNGA3 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2021-04-15). Absent from gnomAD; Associated with achromatopsia 2.

What condition is associated with CNGA3 p.Phe301Ter (c.902_903delinsAA)?

CNGA3 p.Phe301Ter (c.902_903delinsAA) is associated with achromatopsia 2 (ClinVar).

How common is CNGA3 p.Phe301Ter (c.902_903delinsAA) in the general population?

CNGA3 p.Phe301Ter (c.902_903delinsAA) is absent from gnomAD (gnomAD).

How is Achromatopsia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CNGA3 p.Phe301Ter

c.902_903delinsAA · rs1692904914 · VCV988793

Pathogenic/Likely pathogenic No assertion criteria

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

achromatopsia 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (8 of 8) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

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: CNGA3
Protein: p.Phe301Ter
Coding: c.902_903delinsAA
MANE Select: NM_001298
dbSNP: rs1692904914
Type: Indel
Location: chr2:98396072 (GRCh38)
Gene constraint: LOEUF 1.126 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.33 · 10 PDB
Residue 301: an α-helix; the 'ion conduction pathway' region

Full CNGA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

achromatopsia 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Achromatopsia (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

CNGA3 p.Ser111Ter Pathogenic/Likely pathogenic ★★ same condition
CNGA3 p.Ser551_Ile552delinsArgLeu Uncertain significance ★ same condition
CNGA3 p.Cys319fs Likely pathogenic same condition
CNGA3 p.Val437fs Pathogenic same condition
CNGA3 c.216-1G>A Likely pathogenic ★★ same condition
CNGA3 c.396-11C>G Pathogenic/Likely pathogenic ★★ same condition
CNGA3 c.450-1G>A Pathogenic ★★ same condition
CNGA3 p.Ala262Pro Likely pathogenic ★★ ⚠ 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/cnga3-p-phe301ter (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown