STAT1 p.Ser62Ter
c.185C>A · rs2470565458 · VCV3064846
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 25 |
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.27 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 0.78, phastCons 1 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- STAT1
- Protein
- p.Ser62Ter
- Coding
- c.185C>A
- MANE Select
- NM_007315
- dbSNP
- rs2470565458
- Type
- single nucleotide variant
- Location
- chr2:191009051 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 10 PDB
- Residue 62
- an α-helix
Disease context
immunodeficiency 31B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Susceptibility to viral and mycobacterial infections due to STAT1 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
Similar variants
- STAT1 p.Ser62= Likely benign ★★ same residue
- STAT1 p.Ala267Val Pathogenic ★★ ⚠ same condition
- STAT1 p.Arg274Gln Pathogenic ★★ ⚠ same condition
- STAT1 p.Arg274Gly Pathogenic/Likely pathogenic ★★ same condition
- STAT1 p.Arg274Trp Pathogenic ★★ same condition
- STAT1 p.Asp171Asn Likely pathogenic ★★ ⚠ same condition
- STAT1 p.Asp292Glu Likely pathogenic ★★ ⚠ same condition
- STAT1 p.Cys324Arg 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/stat1-p-ser62ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown