Is CEP350 p.Pro796Arg (c.2387C>G) pathogenic?

CEP350 p.Pro796Arg (c.2387C>G) is classified Uncertain significance in CEP350 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-04). AlphaMissense: likely benign (0.2036); Rare (popmax 0.404%, afr).

How common is CEP350 p.Pro796Arg (c.2387C>G) in the general population?

CEP350 p.Pro796Arg (c.2387C>G) is rare (popmax 0.404%, afr) (gnomAD).

What do computational predictors say about CEP350 p.Pro796Arg (c.2387C>G)?

AlphaMissense predicts likely benign (score 0.2036) — an in-silico prediction, not a clinical call.

CEP350 p.Pro796Arg

c.2387C>G · VCV4226242

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2036 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.404%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.2036	likely benign
REVEL	0.09	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 67 kb · p 0.23 · regional, not allelic
Overall
CADD	23.8	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 0.404% African / African-American · 303/75,046 alleles

Filtering AF 0.366% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.352%

Overall 0.0217% 351/1,613,992 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.404%	248
Admixed American	0.0383%	2,609
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0256%	3,905
European (non-Finnish)	0.000593%	168,555

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: CEP350
Protein: p.Pro796Arg
Coding: c.2387C>G
MANE Select: NM_014810
Type: single nucleotide variant
Location: chr1:180020161 (GRCh38)
Gene constraint: LOEUF 0.402 · pLI 1.00 (gnomAD)

Full CEP350 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP350 p.Asp522Gly Benign ★★ same type
CEP350 p.His1462Arg Likely benign ★★ same type
CEP350 p.Ile1905Met Likely benign ★★ same type
CEP350 p.Lys2735Asn Benign ★★ same type
CEP350 c.5567+1G>A Uncertain significance ★ same type
CEP350 p.Ala1096Thr Uncertain significance ★ ⚠ same type
CEP350 p.Ala1160Thr Uncertain significance ★ ⚠ same type
CEP350 p.Ala1163Pro 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/cep350-p-pro796arg (accessed [today's date]).

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