Is GEN1 p.Asp67= (c.201T>C) pathogenic?

GEN1 p.Asp67= (c.201T>C) is classified Likely benign in GEN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-21). No allele count reported in gnomAD v4.1 (AN 1,609,058).

How common is GEN1 p.Asp67= (c.201T>C) in the general population?

GEN1 p.Asp67= (c.201T>C) is no allele count reported in gnomAD v4.1 (AN 1,609,058) (gnomAD).

GEN1 p.Asp67=

c.201T>C · VCV4842193

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 1,609,058)

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 1.9	GERP -0.76, phastCons 1
Overall
CADD	9.867	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,609,058). 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: GEN1
Protein: p.Asp67=
Coding: c.201T>C
MANE Select: NM_001130009
Type: single nucleotide variant
Location: chr2:17761435 (GRCh38)
Gene constraint: LOEUF 1.422 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 61.79 · 1 PDB
Residue 67: the 'xpg-n domain' region

Full GEN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GEN1 p.Asp67Asn Uncertain significance ★ ⚠ same residue
GEN1 p.Asp67Gly Uncertain significance ★ ⚠ same residue
GEN1 p.Asp67Tyr Uncertain significance ★ ⚠ same residue
GEN1 p.Asp67Val Uncertain significance ★ ⚠ same residue
GEN1 c.1264+1G>T Uncertain significance ★★ same type
GEN1 c.953+4A>G Uncertain significance ★★ same type
GEN1 p.Ala135Ser Uncertain significance ★★ ⚠ same type
GEN1 p.Ala197Thr 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/gen1-p-asp67 (accessed [today's date]).

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