CIB2 p.Glu154=
c.462G>A · rs117153558 · VCV197786
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
rare (popmax 0.411%, 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 0.78 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 7.314 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.411%
European (non-Finnish) · 4,852/1,180,032 alleles
Filtering AF
0.401%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.398%
Overall
0.34%
5,489/1,614,212 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.411% | 243 |
| Remaining individualsnot grpmax-eligible | 0.299% | 334 |
| South Asian | 0.273% | 366 |
| Middle Eastern | 0.248% | 404 |
| Ashkenazi Jewishnot grpmax-eligible | 0.122% | 822 |
| Admixed American | 0.0983% | 1,017 |
| African / African-American | 0.0679% | 1,472 |
| Finnishnot grpmax-eligible | 0.0593% | 1,685 |
| East Asian | 0.00446% | 22,439 |
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
- CIB2
- Protein
- p.Glu154=
- Coding
- c.462G>A
- MANE Select
- NM_006383
- dbSNP
- rs117153558
- Type
- single nucleotide variant
- Location
- chr15:78105819 (GRCh38)
- Gene constraint
- LOEUF 1.274 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.71 · 1 PDB
- Residue 154
- a UniProt-annotated variant site (in dfnb48); a UniProt-annotated variant site (in dfnb48; uncertain significance); the ef-hand 3 domain; an α-helix
Similar variants
- CIB2 p.Glu154Lys Uncertain significance ★ same residue
- CIB2 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same type
- CIB2 p.Arg33Ter Pathogenic ★★ same type
- CIB2 p.Arg66Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- CIB2 c.198+3A>G Uncertain significance ★★ same type
- CIB2 p.Ala108Thr Uncertain significance ★★ ⚠ same type
- CIB2 p.Ala76Val Uncertain significance ★★ ⚠ same type
- CIB2 p.Arg134Gln 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/cib2-p-glu154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown