Is CENPT p.Pro98Arg (c.293C>G) pathogenic?

CENPT p.Pro98Arg (c.293C>G) is classified Uncertain significance in CENPT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-28). AlphaMissense: likely benign (0.2263); Absent from gnomAD v4.1.

How common is CENPT p.Pro98Arg (c.293C>G) in the general population?

CENPT p.Pro98Arg (c.293C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CENPT p.Pro98Arg (c.293C>G)?

AlphaMissense predicts likely benign (score 0.2263) — an in-silico prediction, not a clinical call.

CENPT p.Pro98Arg

c.293C>G · rs749906158 · VCV3142431

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2263 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2263	likely benign
REVEL	0.244	benign-leaning
SaProt	LLR -8.34	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.4	GERP 1.7, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 5,589 bp · p 0.92 · regional, not allelic
Overall
CADD	24.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CENPT
Protein: p.Pro98Arg
Coding: c.293C>G
MANE Select: NM_025082
dbSNP: rs749906158
Type: single nucleotide variant
Location: chr16:67832105 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 57.20 · 9 PDB
Residue 98: the 'flexible stalk domain' region

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

Similar variants

CENPT p.Pro98Ala Uncertain significance ★ ⚠ same residue
CENPT p.Pro98Ser Uncertain significance ★ ⚠ same residue
THAP11 p.Ala100Ser Uncertain significance ★★ ⚠ same type
THAP11 p.Asn13Ser Uncertain significance ★★ ⚠ same type
THAP11 p.Asn86Ser Uncertain significance ★★ same type
THAP11 p.Gln104Arg Uncertain significance ★★ ⚠ same type
THAP11 p.Gln168Glu Uncertain significance ★★ ⚠ same type
THAP11 p.Pro170Gln 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/cenpt-p-pro98arg (accessed [today's date]).

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