Is SAMHD1 c.1609del pathogenic?

SAMHD1 c.1609del is classified Likely pathogenic in SAMHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-05). Associated with Aicardi-Goutieres syndrome.

What condition is associated with SAMHD1 c.1609del?

SAMHD1 c.1609del is associated with Aicardi-Goutieres syndrome (ClinVar).

How is Aicardi-Goutières syndrome inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SAMHD1 c.1609del

VCV4815854

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

Aicardi-Goutieres syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.1	GERP 0.2, phastCons 1
Non-coding constraint	Z 1.41	1 kb window · o/e 0.87 · regional · uncalibrated

Variant & gene context

Gene: SAMHD1
Coding: c.1609del
MANE Select: NM_015474
Type: Deletion
Location: chr20:36897959 (GRCh38)
Gene constraint: LOEUF 0.889 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.45 · 76 PDB

Full SAMHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Aicardi-Goutieres syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Aicardi-Goutières syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Antenatal, Infancy, Neonatal
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

SAMHD1 p.Ala529fs Pathogenic/Likely pathogenic ★★ same condition
SAMHD1 p.Glu479fs Pathogenic/Likely pathogenic ★★ same condition
SAMHD1 p.Lys492fs Pathogenic/Likely pathogenic ★★ same condition
SAMHD1 p.Met216fs Pathogenic/Likely pathogenic ★★ same condition
SAMHD1 p.Met505fs Pathogenic/Likely pathogenic ★★ same condition
SAMHD1 p.Val340_Cys341insTer Pathogenic/Likely pathogenic ★★ same condition
SAMHD1 p.Met240fs Likely pathogenic ★ same condition
SAMHD1 c.1270+8del 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/samhd1-c-1609del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown