CNNM4 p.Lys607=
c.1821G>A · rs200000984 · VCV898115
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.359%, eas)
Conditions
1
Jalili syndrome
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 2.8 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 8.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.359%
East Asian · 161/44,886 alleles
Filtering AF
0.313%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.296%
Overall
0.0102%
165/1,614,168 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.359% | 279 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,626 |
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
- CNNM4
- Protein
- p.Lys607=
- Coding
- c.1821G>A
- MANE Select
- NM_020184
- dbSNP
- rs200000984
- Type
- single nucleotide variant
- Location
- chr2:96799196 (GRCh38)
- Gene constraint
- LOEUF 0.794 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.20 · 6 PDB
Similar variants
- CNNM4 p.Arg519Ter Pathogenic ★★ same condition
- CNNM4 p.Gln564Ter Pathogenic ★★ same condition
- CNNM4 p.Gln717Ter Pathogenic/Likely pathogenic ★★ same condition
- CNNM4 c.2130+5G>A Uncertain significance ★★ same condition
- CNNM4 c.*1126G>A Uncertain significance ★★ same condition
- CNNM4 p.Ala598Thr Uncertain significance ★★ ⚠ same condition
- CNNM4 p.Arg523Gln Uncertain significance ★★ ⚠ same condition
- CNNM4 p.Arg651Cys Uncertain significance ★★ ⚠ 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/cnnm4-p-lys607 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown