Is CENPE p.Arg1220Ser (c.3660A>T) pathogenic?

CENPE p.Arg1220Ser (c.3660A>T) is classified Uncertain significance in CENPE (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-04). AlphaMissense: likely benign (0.3056); Very rare (popmax 0.00342%, amr).

How common is CENPE p.Arg1220Ser (c.3660A>T) in the general population?

CENPE p.Arg1220Ser (c.3660A>T) is very rare (popmax 0.00342%, amr) (gnomAD).

What do computational predictors say about CENPE p.Arg1220Ser (c.3660A>T)?

AlphaMissense predicts likely benign (score 0.3056) — an in-silico prediction, not a clinical call.

CENPE p.Arg1220Ser

c.3660A>T · VCV4652122

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3056 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00342%, amr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.3056	likely benign
REVEL	0.042	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 -0.03	GERP -4.1
Regional constraint	o/e 0.97	unconstrained · MANE · 71 kb · p 0.13 · regional, not allelic
Overall
CADD	17.44	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 0.00342% Admixed American · 2/58,466 alleles

Filtering AF 0.000567% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000212%

Overall 0.000138% 2/1,452,746 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: CENPE
Protein: p.Arg1220Ser
Coding: c.3660A>T
MANE Select: NM_001813
Type: single nucleotide variant
Location: chr4:103149145 (GRCh38)
Gene constraint: LOEUF 0.451 · pLI 1.00 (gnomAD)

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

Similar variants

CENPE p.Arg2279Cys Uncertain significance ★★ ⚠ same type
CENPE p.Arg760Ser Uncertain significance ★★ ⚠ same type
CENPE p.Asn1145Lys Uncertain significance ★★ ⚠ same type
CENPE p.Asn1165Ser Uncertain significance ★★ ⚠ same type
CENPE p.Asp1960Tyr Uncertain significance ★★ ⚠ same type
CENPE p.Asp954Asn Uncertain significance ★★ same type
CENPE p.Asp954Tyr Uncertain significance ★★ same type
CENPE p.Gln2022Glu 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/cenpe-p-arg1220ser (accessed [today's date]).

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