Is ERCC2 p.Asn241= (c.723C>T) pathogenic?

ERCC2 p.Asn241= (c.723C>T) is classified Likely benign in ERCC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-02-01). Very rare (popmax 0.00339%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ERCC2 p.Asn241= (c.723C>T)?

ERCC2 p.Asn241= (c.723C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ERCC2 p.Asn241= (c.723C>T) in the general population?

ERCC2 p.Asn241= (c.723C>T) is very rare (popmax 0.00339%, nfe) (gnomAD).

ERCC2 p.Asn241=

c.723C>T · rs746412775 · VCV1757853

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00339%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.109	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.2	GERP -3.5
Overall
CADD	4.568	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00339% European (non-Finnish) · 40/1,180,008 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00225%

Overall 0.00266% 43/1,613,866 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00339%	29,500
Remaining individualsnot grpmax-eligible	0.0032%	31,244
East Asian	0.00223%	44,882

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: ERCC2
Protein: p.Asn241=
Coding: c.723C>T
MANE Select: NM_000400
dbSNP: rs746412775
Type: single nucleotide variant
Location: chr19:45364327 (GRCh38)
Gene constraint: LOEUF 1.089 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 87.74 · 55 PDB
Residue 241: the helicase atp-binding domain; an α-helix

Full ERCC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ERCC2 p.Asn241Thr Uncertain significance ★ ⚠ same residue
MAG p.Val241Glu Uncertain significance ★ ⚠ same residue
MAG p.Val241Met Uncertain significance ★ ⚠ same residue
ERCC2 p.Asn241Ser Uncertain significance ★ ⚠ same residue
MAG p.Val241= Likely benign ★ same residue
ERCC2 p.Ala725Pro Pathogenic/Likely pathogenic ★★ same condition
ERCC2 p.Arg616Pro Pathogenic ★★ same condition
ERCC2 p.Ala108Thr Uncertain significance ★★ ⚠ 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/ercc2-p-asn241 (accessed [today's date]).

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