Is CEP78 p.Ile602Val (c.1804A>G) pathogenic?

CEP78 p.Ile602Val (c.1804A>G) is classified Uncertain significance in CEP78 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-10-05). Ultra-rare (popmax 0.0112%, sas); Associated with Inborn genetic diseases.

What condition is associated with CEP78 p.Ile602Val (c.1804A>G)?

CEP78 p.Ile602Val (c.1804A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CEP78 p.Ile602Val (c.1804A>G) in the general population?

CEP78 p.Ile602Val (c.1804A>G) is ultra-rare (popmax 0.0112%, sas) (gnomAD).

CEP78 p.Ile602Val

c.1804A>G · rs1313881536 · VCV1951913

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0112%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.087	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 1.7, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 34 kb · p 0.014 · regional, not allelic
Overall
CADD	19.12	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0112% South Asian · 9/80,412 alleles

Filtering AF 0.00575% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0043%

Overall 0.00196% 27/1,377,950 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0112%	8,935
Remaining individualsnot grpmax-eligible	0.00368%	27,157
European (non-Finnish)	0.00162%	61,789

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: CEP78
Protein: p.Ile602Val
Coding: c.1804A>G
MANE Select: NM_001330691
dbSNP: rs1313881536
Type: single nucleotide variant
Location: chr9:78265865 (GRCh38)
Gene constraint: LOEUF 1.531 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.28

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 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
CEP78 p.Ala579Val 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-ile602val (accessed [today's date]).

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