CEP112 p.Thr482=
c.1446C>A · rs149063261 · VCV2648111
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.177%, nfe)
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 1.5 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 1.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.177%
European (non-Finnish) · 2,086/1,176,134 alleles
Filtering AF
0.171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.168%
Overall
0.139%
2,238/1,609,280 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.177% | 564 |
| Remaining individualsnot grpmax-eligible | 0.127% | 789 |
| Admixed American | 0.0501% | 1,997 |
| African / African-American | 0.0361% | 2,774 |
| Finnishnot grpmax-eligible | 0.0204% | 4,912 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,560 |
| South Asian | 0.0022% | 45,478 |
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
- CEP112
- Protein
- p.Thr482=
- Coding
- c.1446C>A
- MANE Select
- NM_001199165
- dbSNP
- rs149063261
- Type
- single nucleotide variant
- Location
- chr17:66029180 (GRCh38)
- Gene constraint
- LOEUF 0.91 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.22
- Residue 482
- a UniProt-annotated variant site (in spgf44; likely pathogenic); a UniProt-annotated variant site (in spgf44; likely pathogenic; no protein detected in patient cells)
Similar variants
- CEP112 p.Lys139Arg Uncertain significance ★★ ⚠ same type
- CEP112 p.Lys569Asn Uncertain significance ★★ ⚠ same type
- CEP112 p.Leu937= Benign ★★ same type
- CEP112 c.955+1G>A Likely pathogenic ★ same type
- CEP112 p.Gln418Ter Likely pathogenic ★ same type
- CEP112 p.Ala338Val Uncertain significance ★ ⚠ same type
- CEP112 p.Ala401Gly Uncertain significance ★ ⚠ same type
- CEP112 p.Ala401Val 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/cep112-p-thr482 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown