Is CEP95 p.Arg797Gln (c.2390G>A) pathogenic?

CEP95 p.Arg797Gln (c.2390G>A) is classified Uncertain significance in CEP95 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-02). AlphaMissense: likely benign (0.1001); Very rare (popmax 0.0095%, nfe).

How common is CEP95 p.Arg797Gln (c.2390G>A) in the general population?

CEP95 p.Arg797Gln (c.2390G>A) is very rare (popmax 0.0095%, nfe) (gnomAD).

What do computational predictors say about CEP95 p.Arg797Gln (c.2390G>A)?

AlphaMissense predicts likely benign (score 0.1001) — an in-silico prediction, not a clinical call.

CEP95 p.Arg797Gln

c.2390G>A · rs575666923 · VCV2360222

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1001 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0095%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1001	likely benign
REVEL	0.102	moderately benign-leaning
SaProt	LLR -6.70	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.45	acceptor gain · deltas
Pangolin	Δ0.21	gain · loss 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.5	GERP 2, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 31 kb · p 0.11 · regional, not allelic
Overall
CADD	28.2	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 0.0095% European (non-Finnish) · 112/1,179,438 alleles

Filtering AF 0.00804% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00752%

Overall 0.00775% 125/1,612,946 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0095%	10,531
African / African-American	0.00933%	10,715
Remaining individualsnot grpmax-eligible	0.0048%	20,813
East Asian	0.00223%	44,812
Finnishnot grpmax-eligible	0.00156%	63,976
South Asian	0.0011%	90,826

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: CEP95
Protein: p.Arg797Gln
Coding: c.2390G>A
MANE Select: NM_138363
dbSNP: rs575666923
Type: single nucleotide variant
Location: chr17:64537703 (GRCh38)
Gene constraint: LOEUF 1.061 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.70

Full CEP95 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP95 p.Arg797Trp Uncertain significance ★ ⚠ same residue
CEP95 p.Ala188Val Uncertain significance ★ ⚠ same type
CEP95 p.Ala2Thr Uncertain significance ★ ⚠ same type
CEP95 p.Ala592Glu Uncertain significance ★ ⚠ same type
CEP95 p.Ala601Ser Uncertain significance ★ ⚠ same type
CEP95 p.Ala601Thr Uncertain significance ★ ⚠ same type
CEP95 p.Ala679Val Uncertain significance ★ ⚠ same type
CEP95 p.Arg134Gln 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/cep95-p-arg797gln (accessed [today's date]).

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