CEP19 p.Ser82=
c.246G>A · rs368514311 · VCV1519961
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, afr)
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 0.34 | GERP -1.4, phastCons 0.012 |
| Overall | ||
| CADD | 8.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,888 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00112%
18/1,614,020 alleles · ultra-rare
exomes 7/1,461,884 · genomes 11/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,761 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| East Asian | 0.00223% | 44,900 |
| European (non-Finnish) | 0.000169% | 590,023 |
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.Ser82=
- Coding
- c.246G>A
- MANE Select
- NM_032898
- dbSNP
- rs368514311
- Type
- single nucleotide variant
- Location
- chr3:196707797 (GRCh38)
- Gene constraint
- LOEUF 1.208 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85
Similar variants
- CEP19 p.Ser82Leu Uncertain significance ★★ same residue
- 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
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-ser82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown