CIB1 p.Leu170=
c.510C>T · VCV4722203
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000593%, 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 2.9 | GERP 0.04, phastCons 1 |
| Overall | ||
| CADD | 8.983 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000593%
European (non-Finnish) · 7/1,180,032 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000479%
7/1,461,850 alleles · very rare
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.Leu170=
- Coding
- c.510C>T
- MANE Select
- NM_006384
- Type
- single nucleotide variant
- Location
- chr15:90230978 (GRCh38)
- Gene constraint
- LOEUF 1.233 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.37 · 9 PDB
- Residue 170
- a UniProt-annotated variant site (in ev3; absence of cib1 protein in homozygous patient cells); the ef-hand 2 domain; an α-helix
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-leu170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown