CEP78 p.Met604Val
c.1810A>G · rs771920596 · VCV1404806
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, nfe)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.154 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.20 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 1.08 | unconstrained · MANE · 34 kb · p 0.014 · regional, not allelic |
| Overall | ||
| CADD | 22.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
European (non-Finnish) · 142/1,005,902 alleles
Filtering AF
0.0122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0115%
Overall
0.0108%
151/1,397,014 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0141% | 7,084 |
| Remaining individualsnot grpmax-eligible | 0.0091% | 10,988 |
| South Asian | 0.00371% | 26,940 |
| African / African-American | 0.00143% | 69,998 |
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.Met604Val
- Coding
- c.1810A>G
- MANE Select
- NM_001330691
- dbSNP
- rs771920596
- Type
- single nucleotide variant
- Location
- chr9:78265871 (GRCh38)
- Gene constraint
- LOEUF 1.531 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.28
Similar variants
- CEP78 p.Met604Ile Uncertain significance ★ same residue
- CEP78 p.Leu108Trp Likely pathogenic ★★ same condition
- CEP78 p.Leu150Ser Pathogenic/Likely pathogenic ★★ same condition
- 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
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-met604val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown