COG7 p.Ala565=
c.1695T>C · rs1596915899 · VCV667516
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 -0.67 | GERP -2.1 |
| Overall | ||
| CADD | 1.944 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,040 alleles
Overall
6.84e-05%
1/1,461,884 alleles · very rare
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
- COG7
- Protein
- p.Ala565=
- Coding
- c.1695T>C
- MANE Select
- NM_153603
- dbSNP
- rs1596915899
- Type
- single nucleotide variant
- Location
- chr16:23403802 (GRCh38)
- Gene constraint
- LOEUF 0.651 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 82.77
Similar variants
- COG7 c.318+1G>A Likely pathogenic ★★ same type
- COG7 p.Ala606Asp Pathogenic/Likely pathogenic ★★ ⚠ same type
- COG7 p.Arg444Ter Pathogenic/Likely pathogenic ★★ same type
- COG7 c.1475+4G>A Uncertain significance ★★ same type
- COG7 p.Ala194Val Uncertain significance ★★ ⚠ same type
- COG7 p.Ala20Val Uncertain significance ★★ ⚠ same type
- COG7 p.Ala222Thr Uncertain significance ★★ ⚠ same type
- COG7 p.Ala29Val 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/cog7-p-ala565 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown