CEP135 p.His962=
c.2886T>C · rs554539852 · VCV2704276
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.193%, 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 -1.5 | GERP -3.8 |
| Overall | ||
| CADD | 1.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.193%
South Asian · 176/91,068 alleles
Filtering AF
0.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.161%
Overall
0.0118%
191/1,613,994 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.193% | 517 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| East Asian | 0.00223% | 44,852 |
| Admixed American | 0.00167% | 60,010 |
| African / African-American | 0.00133% | 75,064 |
| European (non-Finnish) | 8.47e-05% | 1,179,988 |
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
- CEP135
- Protein
- p.His962=
- Coding
- c.2886T>C
- MANE Select
- NM_025009
- dbSNP
- rs554539852
- Type
- single nucleotide variant
- Location
- chr4:56017731 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.15 · 2 PDB
Similar variants
- CEP135 p.His962Tyr Uncertain significance ★ ⚠ same residue
- CEP135 c.473-1G>C Likely pathogenic ★★ same type
- CEP135 p.Arg1083Ter Pathogenic/Likely pathogenic ★★ same type
- CEP135 p.Arg292Ter Pathogenic/Likely pathogenic ★★ same type
- CEP135 p.Arg418Ter Pathogenic ★★ same type
- CEP135 p.Arg470Ter Pathogenic/Likely pathogenic ★★ same type
- CEP135 p.Arg908Ter Pathogenic ★★ same type
- CEP135 p.Leu578Ter Pathogenic ★★ 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/cep135-p-his962 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown