CEP19 p.Gln13=
c.39G>A · VCV4708036
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0154%, sas)
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 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 10.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0154%
South Asian · 14/91,090 alleles
Filtering AF
0.00919%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00735%
Overall
0.000867%
14/1,613,988 alleles · ultra-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
- CEP19
- Protein
- p.Gln13=
- Coding
- c.39G>A
- MANE Select
- NM_032898
- Type
- single nucleotide variant
- Location
- chr3:196708619 (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-gln13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown