Is STAT6 p.Trp39Ter (c.116G>A) pathogenic?

STAT6 p.Trp39Ter (c.116G>A) is classified Uncertain significance in STAT6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-05). No allele count reported in gnomAD v4.1 (AN 1,592,790).

How common is STAT6 p.Trp39Ter (c.116G>A) in the general population?

STAT6 p.Trp39Ter (c.116G>A) is no allele count reported in gnomAD v4.1 (AN 1,592,790) (gnomAD).

STAT6 p.Trp39Ter

c.116G>A · VCV4917288

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,592,790)

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
NMD	predicted	premature termination codon in exon 2 of 22
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.6	GERP 0.82, phastCons 1
Overall
CADD	44.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,592,790). 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: STAT6
Protein: p.Trp39Ter
Coding: c.116G>A
MANE Select: NM_003153
Type: single nucleotide variant
Location: chr12:57108163 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.56 (gnomAD)
Structure: AlphaFold pLDDT 77.44 · 7 PDB

Full STAT6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

STAT6 c.1001+10G>A Benign ★★ same type
STAT6 c.1213-6C>T Benign ★★ same type
STAT6 c.1744+9A>C Likely benign ★★ same type
STAT6 p.Ser564= Benign/Likely benign ★★ same type
STAT6 p.Val269Ile Benign ★★ same type
STAT6 p.Asp419His Likely pathogenic ★ same type
STAT6 p.Ala109Val Uncertain significance ★ ⚠ same type
STAT6 p.Ala245Val 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/stat6-p-trp39ter (accessed [today's date]).

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