Is CEP83 p.Gln689fs (c.2065_2075del) pathogenic?

CEP83 p.Gln689fs (c.20652075del) is classified Uncertain significance in CEP83 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-26). Absent from gnomAD; Associated with nephronophthisis 18.

What condition is associated with CEP83 p.Gln689fs (c.2065_2075del)?

CEP83 p.Gln689fs (c.2065_2075del) is associated with nephronophthisis 18 (ClinVar).

How common is CEP83 p.Gln689fs (c.2065_2075del) in the general population?

CEP83 p.Gln689fs (c.2065_2075del) is absent from gnomAD (gnomAD).

How is Nephronophthisis inherited?

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

CEP83 p.Gln689fs

c.2065_2075del · rs1969370890 · VCV1023907

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

nephronophthisis 18

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 (17 of 17) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.16	GERP -4.6, phastCons 0.71

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: CEP83
Protein: p.Gln689fs
Coding: c.2065_2075del
MANE Select: NM_016122
dbSNP: rs1969370890
Type: Deletion
Location: chr12:94308844 (GRCh38)
Gene constraint: LOEUF 0.807 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.90

Full CEP83 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nephronophthisis 18 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Nephronophthisis (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Finland)

Similar variants

CEP83 p.Gln689Arg Uncertain significance ★ ⚠ same residue
CEP83 p.Glu669fs Pathogenic ★★ same condition
CEP83 p.Ala556fs Likely pathogenic ★ same condition
CEP83 p.Arg514fs Pathogenic ★ same condition
CEP83 p.Asp354fs Pathogenic ★ same condition
CEP83 p.Glu437fs Pathogenic ★ same condition
CEP83 p.Leu203fs Pathogenic ★ same condition
CEP83 p.Lys390fs 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/cep83-p-gln689fs (accessed [today's date]).

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