CILP p.Asp647=
c.1941C>T · rs199911017 · VCV3033239
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0556%, nfe)
Conditions
1
CILP-related disorder
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 -2.4 | GERP -3.4 |
| Overall | ||
| CADD | 0.873 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0556%
European (non-Finnish) · 656/1,180,038 alleles
Filtering AF
0.052%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0506%
Overall
0.0437%
705/1,614,100 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0556% | 1,799 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| African / African-American | 0.012% | 8,326 |
| Finnishnot grpmax-eligible | 0.00781% | 12,808 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Admixed American | 0.00333% | 30,008 |
| East Asian | 0.00223% | 44,898 |
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
- CILP
- Protein
- p.Asp647=
- Coding
- c.1941C>T
- MANE Select
- NM_003613
- dbSNP
- rs199911017
- Type
- single nucleotide variant
- Location
- chr15:65198345 (GRCh38)
- Gene constraint
- LOEUF 1.077 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.30
Disease context
CILP-related disorder
Similar variants
- CILP p.Arg431Cys Benign ⚠ same condition
- CILP p.Arg448His Benign same condition
- CILP p.Gln979Arg Benign same condition
- CILP p.Gly1166Ser Benign same condition
- CILP p.Gly69= Likely benign same condition
- CILP p.Thr1078= Likely benign same condition
- CILP p.Thr486= Likely benign same condition
- CILP p.Thr486Met Benign same condition
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/cilp-p-asp647 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown