Is ERCC2 p.Pro64Leu (c.191C>T) pathogenic?

ERCC2 p.Pro64Leu (c.191C>T) is classified Uncertain significance in ERCC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-17). AlphaMissense: ambiguous (0.4666); Very rare (popmax 0.00445%, eas); Associated with Inborn genetic diseases.

What condition is associated with ERCC2 p.Pro64Leu (c.191C>T)?

ERCC2 p.Pro64Leu (c.191C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ERCC2 p.Pro64Leu (c.191C>T) in the general population?

ERCC2 p.Pro64Leu (c.191C>T) is very rare (popmax 0.00445%, eas) (gnomAD).

What do computational predictors say about ERCC2 p.Pro64Leu (c.191C>T)?

AlphaMissense predicts ambiguous (score 0.4666) — an in-silico prediction, not a clinical call.

ERCC2 p.Pro64Leu

c.191C>T · rs773453200 · VCV1782636

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4666 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00445%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4666	ambiguous
REVEL	0.48	indeterminate
SaProt	LLR -13.79	damaging
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP 12	GERP 1.6, phastCons 1
Regional constraint	o/e 0.47	unconstrained · MANE · 1,402 bp · p 2.6e-05 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00445% East Asian · 2/44,900 alleles

Filtering AF 0.000738% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000276%

Overall 0.000186% 3/1,614,078 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00445%	22,450
African / African-American	0.00133%	74,918

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.Pro64Leu
Coding: c.191C>T
MANE Select: NM_000400
dbSNP: rs773453200
Type: single nucleotide variant
Location: chr19:45368985 (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 64: the helicase atp-binding domain; a turn

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.Pro64= Likely benign ★★ same residue
MAG p.Pro64Ser Uncertain significance ★ ⚠ same residue
ERCC2 p.Ala725Pro Pathogenic/Likely pathogenic ★★ same condition
ERCC2 p.Arg616Pro Pathogenic ★★ same condition
ERCC2 p.Ala108Thr Uncertain significance ★★ ⚠ same condition
ERCC2 p.Ala144Val Uncertain significance ★★ ⚠ same condition
ERCC2 p.Ala226Thr Uncertain significance ★★ ⚠ same condition
ERCC2 p.Ala306Val 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-pro64leu (accessed [today's date]).

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