Is GTF2E2 p.Ser34= (c.102A>G) pathogenic?

GTF2E2 p.Ser34= (c.102A>G) is classified Likely benign in GTF2E2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). No allele count reported in gnomAD v4.1 (AN 1,607,602).

How common is GTF2E2 p.Ser34= (c.102A>G) in the general population?

GTF2E2 p.Ser34= (c.102A>G) is no allele count reported in gnomAD v4.1 (AN 1,607,602) (gnomAD).

GTF2E2 p.Ser34=

c.102A>G · rs113662547 · VCV2018190

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,607,602)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.96	GERP -5.4, phastCons 0.001
Overall
CADD	2.713	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,607,602). 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: GTF2E2
Protein: p.Ser34=
Coding: c.102A>G
MANE Select: NM_002095
dbSNP: rs113662547
Type: single nucleotide variant
Location: chr8:30653497 (GRCh38)
Gene constraint: LOEUF 1.107 · pLI 0.40 (gnomAD)
Structure: AlphaFold pLDDT 68.97 · 46 PDB
Residue 34: the 'disordered' region

Full GTF2E2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GTF2E2 p.Ser34Leu Uncertain significance ★ ⚠ same residue
GTF2E2 p.Ala138Thr Uncertain significance ★★ ⚠ same type
GTF2E2 p.Ala278Ser Uncertain significance ★★ ⚠ same type
GTF2E2 p.Arg25Cys Uncertain significance ★★ ⚠ same type
GTF2E2 p.Arg269Cys Uncertain significance ★★ ⚠ same type
GTF2E2 p.Gly47Ala Uncertain significance ★★ ⚠ same type
GTF2E2 p.His158Arg Uncertain significance ★★ ⚠ same type
GTF2E2 p.Lys197Arg 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/gtf2e2-p-ser34 (accessed [today's date]).

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