Is CEP83 p.Arg279= (c.837T>C) pathogenic?

CEP83 p.Arg279= (c.837T>C) is classified Benign in CEP83 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-04). Common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele; Associated with nephronophthisis 18.

What condition is associated with CEP83 p.Arg279= (c.837T>C)?

CEP83 p.Arg279= (c.837T>C) is associated with nephronophthisis 18 (ClinVar).

How is Nephronophthisis inherited?

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

CEP83 p.Arg279=

Q: How common is CEP83 p.Arg279= (c.837T>C) in the general population?

CEP83 p.Arg279= (c.837T>C) is common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.837T>C · rs4761611 · VCV1164811

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

nephronophthisis 18

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP -2.5, phastCons 1
Overall
CADD	7.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 98.1% East Asian · 42,303/43,104 alleles

Filtering AF 97.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 97%

Overall 68% 1,057,878/1,554,982 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	98.1%	1
African / African-American	94.3%	1
Admixed American	80.7%	1
Finnishnot grpmax-eligible	72.2%	1
Remaining individualsnot grpmax-eligible	69.1%	1
South Asian	68.1%	1
Amishnot grpmax-eligible	65.5%	2
European (non-Finnish)	64.6%	2
Middle Eastern	61.6%	2
Ashkenazi Jewishnot grpmax-eligible	58.7%	2

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.Arg279=
Coding: c.837T>C
MANE Select: NM_016122
dbSNP: rs4761611
Type: single nucleotide variant
Location: chr12:94375982 (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.Arg279His 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-arg279 (accessed [today's date]).

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