Is CEP83 p.Lys384Arg (c.1151A>G) pathogenic?

CEP83 p.Lys384Arg (c.1151A>G) is classified Conflicting classifications of pathogenicity in CEP83 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.0732); Rare (popmax 0.112%, nfe); Associated with nephronophthisis 18.

What condition is associated with CEP83 p.Lys384Arg (c.1151A>G)?

CEP83 p.Lys384Arg (c.1151A>G) is associated with nephronophthisis 18 (ClinVar).

How common is CEP83 p.Lys384Arg (c.1151A>G) in the general population?

CEP83 p.Lys384Arg (c.1151A>G) is rare (popmax 0.112%, nfe) (gnomAD).

How is Nephronophthisis inherited?

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

What do computational predictors say about CEP83 p.Lys384Arg (c.1151A>G)?

AlphaMissense predicts likely benign (score 0.0732) — an in-silico prediction, not a clinical call.

CEP83 p.Lys384Arg

c.1151A>G · rs185058802 · VCV841958

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0732 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.112%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

nephronophthisis 18

Computational evidence

Protein change
AlphaMissense	0.0732	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -7.18	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP 0.1, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 104 kb · p 0.01 · regional, not allelic
Overall
CADD	16.59	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.112% European (non-Finnish) · 1,321/1,179,696 alleles

Filtering AF 0.107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.105%

Overall 0.0854% 1,378/1,613,562 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.112%	893
Remaining individualsnot grpmax-eligible	0.0528%	1,893
Middle Eastern	0.0495%	2,019
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,861
Admixed American	0.01%	10,000
African / African-American	0.00666%	15,008
Finnishnot grpmax-eligible	0.00469%	21,331
South Asian	0.0044%	22,744

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: CEP83
Protein: p.Lys384Arg
Coding: c.1151A>G
MANE Select: NM_016122
dbSNP: rs185058802
Type: single nucleotide variant
Location: chr12:94368099 (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.Arg209Ter Pathogenic/Likely pathogenic ★★ same condition
CEP83 p.Arg215Ter Pathogenic/Likely pathogenic ★★ same condition
CEP83 p.Arg511Pro Pathogenic/Likely pathogenic ★★ same condition
CEP83 p.Arg511Ter Pathogenic/Likely pathogenic ★★ same condition
CEP83 p.Gln81Ter Pathogenic/Likely pathogenic ★★ same condition
CEP83 p.Leu351Ter Pathogenic/Likely pathogenic ★★ same condition
CEP83 p.Ala232Val Uncertain significance ★★ ⚠ same condition
CEP83 p.Ala243Val 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/cep83-p-lys384arg (accessed [today's date]).

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