STAT4 p.Asn456=
c.1368T>C · rs778632183 · VCV1530844
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.122%, sas)
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 0.072 | GERP -3.6, phastCons 0.04 |
| Overall | ||
| CADD | 4.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.122%
South Asian · 111/91,090 alleles
Filtering AF
0.103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0965%
Overall
0.00905%
146/1,614,082 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.122% | 821 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| European (non-Finnish) | 0.00195% | 51,305 |
| African / African-American | 0.00133% | 74,936 |
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
- STAT4
- Protein
- p.Asn456=
- Coding
- c.1368T>C
- MANE Select
- NM_003151
- dbSNP
- rs778632183
- Type
- single nucleotide variant
- Location
- chr2:191039265 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.93 (gnomAD)
- Structure
- AlphaFold pLDDT 86.87
Similar variants
- STAT4 p.Asn456Lys Uncertain significance ★ ⚠ same residue
- STAT4 p.Ala245Thr Uncertain significance ★★ ⚠ same type
- STAT4 p.Arg241Gln Uncertain significance ★★ ⚠ same type
- STAT4 p.Arg70Leu Uncertain significance ★★ ⚠ same type
- STAT4 p.Arg87Lys Uncertain significance ★★ ⚠ same type
- STAT4 p.Asp513Val Uncertain significance ★★ ⚠ same type
- STAT4 p.Cys323Arg Uncertain significance ★★ ⚠ same type
- STAT4 p.Gln243Lys 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/stat4-p-asn456 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown