CIB1 p.Asp119=
c.357T>C · rs755078702 · VCV1625461
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00231%, 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 -2.3 | GERP -2.8 |
| Overall | ||
| CADD | 3.845 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00231%
European (non-Finnish) · 27/1,170,800 alleles
Filtering AF
0.00158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00183%
29/1,588,152 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00231% | 43,363 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,122 |
| South Asian | 0.00112% | 89,548 |
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
- CIB1
- Protein
- p.Asp119=
- Coding
- c.357T>C
- MANE Select
- NM_006384
- dbSNP
- rs755078702
- Type
- single nucleotide variant
- Location
- chr15:90231203 (GRCh38)
- Gene constraint
- LOEUF 1.233 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.37 · 9 PDB
- Residue 119
- a UniProt-annotated variant site (in ev3; absence of cib1 protein in homozygous patient cells); the ef-hand 1 domain
Similar variants
- CIB1 p.Asp119Gly Uncertain significance ★ ⚠ same residue
- GDPGP1 p.Phe119Ser Uncertain significance ★ ⚠ same residue
- CIB1 p.Ala184Pro Uncertain significance ★★ ⚠ same type
- CIB1 p.Ala66Thr Uncertain significance ★★ ⚠ same type
- CIB1 p.Arg113His Uncertain significance ★★ ⚠ same type
- CIB1 p.Arg143Gln Uncertain significance ★★ ⚠ same type
- CIB1 p.Arg143Trp Uncertain significance ★★ ⚠ same type
- CIB1 p.Arg72Gln 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/cib1-p-asp119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown