CEP19 p.Phe74=
c.222C>T · rs191514031 · VCV1552563
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0417%, amr)
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 0.55 | GERP -2.8, phastCons 0.031 |
| Overall | ||
| CADD | 3.749 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0417%
Admixed American · 25/60,004 alleles
Filtering AF
0.0289%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0247%
Overall
0.0018%
29/1,614,112 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0417% | 2,400 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
| European (non-Finnish) | 8.47e-05% | 1,180,020 |
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
- CEP19
- Protein
- p.Phe74=
- Coding
- c.222C>T
- MANE Select
- NM_032898
- dbSNP
- rs191514031
- Type
- single nucleotide variant
- Location
- chr3:196707821 (GRCh38)
- Gene constraint
- LOEUF 1.208 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85
Similar variants
- CEP19 p.Arg32His Uncertain significance ★★ same type
- CEP19 p.Arg37Ter Uncertain significance ★★ same type
- CEP19 p.Arg95Trp Uncertain significance ★★ same type
- CEP19 p.Asn54Ser Uncertain significance ★★ same type
- CEP19 p.Gly27Arg Uncertain significance ★★ same type
- CEP19 p.Ile33Val Uncertain significance ★★ same type
- CEP19 p.Lys111Arg Uncertain significance ★★ same type
- CEP19 p.Met1Thr 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/cep19-p-phe74 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown