Is CEP83 p.Arg374Cys (c.1120C>T) pathogenic?

CEP83 p.Arg374Cys (c.1120C>T) is classified Uncertain significance in CEP83 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-06-07). AlphaMissense: likely benign (0.2238); Ultra-rare (popmax 0.0756%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CEP83 p.Arg374Cys (c.1120C>T)?

CEP83 p.Arg374Cys (c.1120C>T) is associated with Inborn genetic diseases, nephronophthisis 18 (ClinVar).

How common is CEP83 p.Arg374Cys (c.1120C>T) in the general population?

CEP83 p.Arg374Cys (c.1120C>T) is ultra-rare (popmax 0.0756%, nfe) (gnomAD).

What do computational predictors say about CEP83 p.Arg374Cys (c.1120C>T)?

AlphaMissense predicts likely benign (score 0.2238) — an in-silico prediction, not a clinical call.

CEP83 p.Arg374Cys

c.1120C>T · rs200860374 · VCV652817

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.2238 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0756%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2238	likely benign
REVEL	0.407	indeterminate
SaProt	LLR -9.02	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 104 kb · p 0.01 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0756% European (non-Finnish) · 891/1,178,728 alleles

Filtering AF 0.0714% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0698%

Overall 0.0615% 991/1,612,330 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0756%	1,323
Admixed American	0.0617%	1,621
Remaining individualsnot grpmax-eligible	0.0417%	2,401
South Asian	0.0253%	3,956
Middle Eastern	0.0165%	6,058
Finnishnot grpmax-eligible	0.00939%	10,650
African / African-American	0.008%	12,494
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,568

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.Arg374Cys
Coding: c.1120C>T
MANE Select: NM_016122
dbSNP: rs200860374
Type: single nucleotide variant
Location: chr12:94368130 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: nephronophthisis 18

Similar variants

CEP83 p.Arg374Gly Uncertain significance ★ ⚠ same residue
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

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-arg374cys (accessed [today's date]).

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