CMIP p.Lys559=
c.1677A>G · rs527523022 · VCV739625
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.155%, 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 -0.14 | GERP -5.1, phastCons 0.011 |
| Overall | ||
| CADD | 4.155 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.155%
South Asian · 141/91,030 alleles
Filtering AF
0.134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.126%
Overall
0.00936%
151/1,613,750 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.155% | 646 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,925 |
| African / African-American | 0.00133% | 75,010 |
| European (non-Finnish) | 0.00017% | 589,890 |
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
- CMIP
- Protein
- p.Lys559=
- Coding
- c.1677A>G
- MANE Select
- NM_198390
- dbSNP
- rs527523022
- Type
- single nucleotide variant
- Location
- chr16:81699723 (GRCh38)
- Gene constraint
- LOEUF 0.189 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.52
Similar variants
- CMIP c.1638+10G>A Likely benign ★★ same type
- CMIP c.2269-10C>T Benign/Likely benign ★★ same type
- CMIP p.Asn295= Benign ★★ same type
- CMIP p.Leu369= Likely benign ★★ same type
- CMIP p.Pro414= Benign ★★ same type
- CMIP p.Val547= Benign ★★ same type
- CMIP c.1035-1G>A Uncertain significance ★ same type
- CMIP p.Ala113Thr 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/cmip-p-lys559 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown