CIB1 p.Thr79=
c.237A>G · rs1011455379 · VCV2811744
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -8.2 | GERP -2.8 |
| Overall | ||
| CADD | 0.566 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,912 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000186%
3/1,614,054 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,456 |
| European (non-Finnish) | 8.47e-05% | 1,180,038 |
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.Thr79=
- Coding
- c.237A>G
- MANE Select
- NM_006384
- dbSNP
- rs1011455379
- Type
- single nucleotide variant
- Location
- chr15:90231466 (GRCh38)
- Gene constraint
- LOEUF 1.233 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.37 · 9 PDB
- Residue 79
- a UniProt-annotated variant site (in ev3; absence of cib1 protein in homozygous patient cells)
Similar variants
- CIB1 p.Thr79fs Pathogenic ★ 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
- CIB1 p.Asn155Asp 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-thr79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown