SAMHD1 p.Glu166=
c.498G>A · rs2063594220 · VCV2851359
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Aicardi-Goutieres syndrome 5
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 -1.2 | GERP -3.8, phastCons 0.001 |
| Overall | ||
| CADD | 6.542 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SAMHD1
- Protein
- p.Glu166=
- Coding
- c.498G>A
- MANE Select
- NM_015474
- dbSNP
- rs2063594220
- Type
- single nucleotide variant
- Location
- chr20:36935040 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.45 · 76 PDB
- Residue 166
- an α-helix; the hd domain
Disease context
Aicardi-Goutieres syndrome 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: Aicardi-Goutieres syndrome
For Aicardi-Goutières syndrome (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Antenatal, Infancy, Neonatal
- Prevalence
- 1-5 / 10 000 (Europe)
Similar variants
- SAMHD1 p.Glu166fs Pathogenic ★ same residue
- SAMHD1 c.1062+1G>T Pathogenic/Likely pathogenic ★★ same condition
- SAMHD1 c.1411-2A>G Pathogenic ★★ same condition
- SAMHD1 c.509+1G>A Likely pathogenic ★★ same condition
- SAMHD1 c.626-1G>C Pathogenic/Likely pathogenic ★★ same condition
- SAMHD1 p.Arg106Ter Pathogenic/Likely pathogenic ★★ same condition
- SAMHD1 p.Arg134Ter Pathogenic/Likely pathogenic ★★ same condition
- SAMHD1 p.Arg143Cys 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/samhd1-p-glu166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown