Is CEP78 p.Pro587Ser (c.1759C>T) pathogenic?

CEP78 p.Pro587Ser (c.1759C>T) is classified Likely benign in CEP78 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-01). AlphaMissense: likely benign (0.0719); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CEP78 p.Pro587Ser (c.1759C>T)?

CEP78 p.Pro587Ser (c.1759C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEP78 p.Pro587Ser (c.1759C>T) in the general population?

CEP78 p.Pro587Ser (c.1759C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CEP78 p.Pro587Ser (c.1759C>T)?

AlphaMissense predicts likely benign (score 0.0719) — an in-silico prediction, not a clinical call.

CEP78 p.Pro587Ser

c.1759C>T · VCV4226507

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0719 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0719	likely benign
REVEL	0.027	moderately benign-leaning
SaProt	LLR -6.04	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 -1.1	GERP -3.5
Regional constraint	o/e 1.08	unconstrained · MANE · 34 kb · p 0.014 · regional, not allelic
Overall
CADD	2.705	PHRED · no single calibrated threshold — expert panels disagree

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: CEP78
Protein: p.Pro587Ser
Coding: c.1759C>T
MANE Select: NM_001330691
Type: single nucleotide variant
Location: chr9:78265505 (GRCh38)
Gene constraint: LOEUF 1.531 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.28
Residue 587: the 'disordered' region

Full CEP78 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEP78 p.Pro587Leu Uncertain significance ★★ ⚠ same residue
CEP78 c.2107+37C>T Uncertain significance ★★ same condition
CEP78 p.Ala304Thr Uncertain significance ★★ ⚠ same condition
CEP78 p.Ala378Val Uncertain significance ★★ ⚠ same condition
CEP78 p.Ala380Ser Uncertain significance ★★ ⚠ same condition
CEP78 p.Ala380Thr Uncertain significance ★★ ⚠ same condition
CEP78 p.Ala47Thr Uncertain significance ★★ ⚠ same condition
CEP78 p.Ala56Val Uncertain significance ★★ ⚠ same condition

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/cep78-p-pro587ser (accessed [today's date]).

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