Is CEP170B p.Pro789Arg (c.2366C>G) pathogenic?

CEP170B p.Pro789Arg (c.2366C>G) is classified Uncertain significance in CEP170B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-01). Very rare (popmax 0.000528%, nfe).

How common is CEP170B p.Pro789Arg (c.2366C>G) in the general population?

CEP170B p.Pro789Arg (c.2366C>G) is very rare (popmax 0.000528%, nfe) (gnomAD).

CEP170B p.Pro789Arg

c.2366C>G · rs752099032 · VCV2514030

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000528%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.02	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.81	GERP -0.7
Regional constraint	o/e 1.00	unconstrained · MANE · 19 kb · p 0.99 · regional, not allelic
Overall
CADD	14.08	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000528% European (non-Finnish) · 6/1,136,392 alleles

Filtering AF 0.00019% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000125%

Overall 0.000395% 6/1,519,114 alleles · very rare

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: CEP170B
Protein: p.Pro789Arg
Coding: c.2366C>G
MANE Select: NM_001112726
dbSNP: rs752099032
Type: single nucleotide variant
Location: chr14:104886605 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.31
Residue 789: the 'disordered' region

Full CEP170B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP170B p.Lys368Glu Uncertain significance ★★ same type
CEP170B p.Pro148Leu Uncertain significance ★★ same type
CEP170B p.Ala259Val Benign ★★ same type
CEP170B p.Arg147= Benign ★★ same type
CEP170B p.Ala1053Val Uncertain significance ★ same type
CEP170B p.Ala1062Val Uncertain significance ★ same type
CEP170B p.Ala1083Val Uncertain significance ★ same type
CEP170B p.Ala1091Thr Uncertain significance ★ 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/cep170b-p-pro789arg (accessed [today's date]).

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