CIB1 p.Asp120=
c.360C>T · VCV3719339
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0389%, 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 -1.1 | GERP -2.8 |
| Overall | ||
| CADD | 8.657 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0389%
South Asian · 35/89,988 alleles
Filtering AF
0.0287%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0252%
Overall
0.00532%
85/1,597,722 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0389% | 2,571 |
| European (non-Finnish) | 0.00374% | 26,703 |
| Admixed American | 0.0035% | 28,578 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,123 |
| African / African-American | 0.00281% | 35,539 |
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.Asp120=
- Coding
- c.360C>T
- MANE Select
- NM_006384
- Type
- single nucleotide variant
- Location
- chr15:90231200 (GRCh38)
- Gene constraint
- LOEUF 1.233 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.37 · 9 PDB
- Residue 120
- a UniProt-annotated variant site (in ev3; absence of cib1 protein in homozygous patient cells); the ef-hand 1 domain; a β-strand; a binding site
Similar variants
- 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
- CIB1 p.Asn155Asp Uncertain significance ★★ ⚠ same type
- CIB1 p.Asn169Ser 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-asp120 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown