Is CNGA3 p.Asp442Phe (c.1324_1325delinsTT) pathogenic?

CNGA3 p.Asp442Phe (c.13241325delinsTT) is classified Uncertain significance in CNGA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-07). Absent from gnomAD.

How common is CNGA3 p.Asp442Phe (c.1324_1325delinsTT) in the general population?

CNGA3 p.Asp442Phe (c.1324_1325delinsTT) is absent from gnomAD (gnomAD).

CNGA3 p.Asp442Phe

c.1324_1325delinsTT · rs1692918521 · VCV956725

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 1,336 bp · p 0.34 · regional, not allelic

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.Asp442Phe
Coding: c.1324_1325delinsTT
MANE Select: NM_001298
dbSNP: rs1692918521
Type: Indel
Location: chr2:98396494 (GRCh38)
Gene constraint: LOEUF 1.126 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.33 · 10 PDB
Residue 442: an α-helix; the 'c-linker' region

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

Similar variants

CNGA3 p.Asp442Glu Uncertain significance ★ same residue
CNGA3 p.Asp442His Uncertain significance ★ same residue
CNGA3 p.Ser111Ter Pathogenic/Likely pathogenic ★★ same type
CNGA3 c.566_566+1delinsAT Likely pathogenic ★ same type
CNGA3 c.567-13_567-12delinsCA Uncertain significance ★ same type
CNGA3 p.Ser551_Ile552delinsArgLeu Uncertain significance ★ same type
CNGA3 p.Cys319fs Likely pathogenic same type
CNGA3 p.Phe301Ter 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/cnga3-p-asp442phe (accessed [today's date]).

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