COG5 p.Ala173=
c.519T>C · rs773484910 · VCV2029818
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,595,640)
Conditions
1
COG5-congenital disorder of glycosylation
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 1.8 | GERP -4.3, phastCons 1 |
| Overall | ||
| CADD | 8.702 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,595,640). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- COG5
- Protein
- p.Ala173=
- Coding
- c.519T>C
- MANE Select
- NM_006348
- dbSNP
- rs773484910
- Type
- single nucleotide variant
- Location
- chr7:107527256 (GRCh38)
- Gene constraint
- LOEUF 1.026 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37
Disease context
COG5-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor COG5-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
Similar variants
- COG5 c.1475+1G>A Likely pathogenic ★★ same condition
- COG5 c.2295+2T>C Pathogenic/Likely pathogenic ★★ same condition
- COG5 p.Arg205Ter Pathogenic ★★ same condition
- COG5 p.Arg283Ter Pathogenic ★★ same condition
- COG5 p.Arg461Ter Pathogenic/Likely pathogenic ★★ same condition
- COG5 p.Arg690Ter Pathogenic/Likely pathogenic ★★ same condition
- COG5 p.Arg708Ter Pathogenic/Likely pathogenic ★★ same condition
- COG5 p.Met1Arg Pathogenic/Likely pathogenic ★★ ⚠ 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/cog5-p-ala173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown