CIMAP1D p.Ala69=
c.207C>A · rs143177865 · VCV916329
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0865%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 7.047 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0865%
Middle Eastern · 5/5,782 alleles
Filtering AF
0.0403%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0356%
Overall
0.00434%
67/1,545,182 alleles · ultra-rare
exomes 38/1,392,880 · genomes 29/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0865% | 1,156 |
| African / African-American | 0.0536% | 1,867 |
| Admixed American | 0.0178% | 5,626 |
| Remaining individualsnot grpmax-eligible | 0.00669% | 14,957 |
| South Asian | 0.0012% | 83,640 |
| European (non-Finnish) | 0.000787% | 127,131 |
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
- CIMAP1D
- Protein
- p.Ala69=
- Coding
- c.207C>A
- MANE Select
- NM_182577
- dbSNP
- rs143177865
- Type
- single nucleotide variant
- Location
- chr19:472422 (GRCh38)
- Structure
- AlphaFold pLDDT 67.70
Similar variants
- CIMAP1D p.Ala255Ser Uncertain significance ★ ⚠ same type
- CIMAP1D p.Ala66Thr Uncertain significance ★ ⚠ same type
- CIMAP1D p.Arg101Cys Uncertain significance ★ ⚠ same type
- CIMAP1D p.Arg11Gln Uncertain significance ★ ⚠ same type
- CIMAP1D p.Arg11Trp Uncertain significance ★ ⚠ same type
- CIMAP1D p.Arg136His Uncertain significance ★ ⚠ same type
- CIMAP1D p.Arg138Trp Uncertain significance ★ ⚠ same type
- CIMAP1D p.Arg148Cys 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/cimap1d-p-ala69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown