Is CEP57 p.Thr96= (c.288C>T) pathogenic?

CEP57 p.Thr96= (c.288C>T) is classified Likely benign in CEP57 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-01). Very rare (popmax 0.000593%, nfe).

How common is CEP57 p.Thr96= (c.288C>T) in the general population?

CEP57 p.Thr96= (c.288C>T) is very rare (popmax 0.000593%, nfe) (gnomAD).

CEP57 p.Thr96=

c.288C>T · VCV4822620

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000593%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -3.1
Overall
CADD	7.615	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000593% European (non-Finnish) · 7/1,179,940 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000479% 7/1,461,670 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: CEP57
Protein: p.Thr96=
Coding: c.288C>T
MANE Select: NM_014679
Type: single nucleotide variant
Location: chr11:95813017 (GRCh38)
Gene constraint: LOEUF 0.74 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.32 · 3 PDB
Residue 96: the 'centrosome localization domain (cld)' region

Full CEP57 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP57 p.Thr96Ala Uncertain significance ★ ⚠ same residue
CEP57 p.Thr96Ser Uncertain significance ★ ⚠ same residue
CEP57 p.Arg339Ter Pathogenic ★★ same type
CEP57 c.202+6C>T Uncertain significance ★★ same type
CEP57 p.Ala19Gly Uncertain significance ★★ ⚠ same type
CEP57 p.Ala278Thr Uncertain significance ★★ ⚠ same type
CEP57 p.Ala278Val Uncertain significance ★★ ⚠ same type
CEP57 p.Ala412Thr 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/cep57-p-thr96 (accessed [today's date]).

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