Is NOTCH2 p.Asp813= (c.2439C>T) pathogenic?

NOTCH2 p.Asp813= (c.2439C>T) is classified Likely benign in NOTCH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-25). Very rare (popmax 0.00333%, amr); Associated with acroosteolysis dominant type.

What condition is associated with NOTCH2 p.Asp813= (c.2439C>T)?

NOTCH2 p.Asp813= (c.2439C>T) is associated with acroosteolysis dominant type (ClinVar).

How common is NOTCH2 p.Asp813= (c.2439C>T) in the general population?

NOTCH2 p.Asp813= (c.2439C>T) is very rare (popmax 0.00333%, amr) (gnomAD).

NOTCH2 p.Asp813=

c.2439C>T · rs781994761 · VCV2056455

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

Conditions

acroosteolysis dominant type

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.097
Overall
CADD	7.263	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00333% Admixed American · 2/60,016 alleles

Filtering AF 0.00188% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00164%

Overall 0.00217% 35/1,613,966 alleles · very rare exomes 32/1,461,730 · genomes 3/152,236 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00333%	30,008
Remaining individualsnot grpmax-eligible	0.0032%	31,238
European (non-Finnish)	0.00263%	38,062

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: NOTCH2
Protein: p.Asp813=
Coding: c.2439C>T
MANE Select: NM_024408
dbSNP: rs781994761
Type: single nucleotide variant
Location: chr1:119950764 (GRCh38)
Gene constraint: LOEUF 0.151 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 59.51 · 2 PDB
Residue 813: the egf-like 21; calcium-binding domain

Full NOTCH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

acroosteolysis dominant type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NOTCH2 p.Asp813Glu Uncertain significance ★ ⚠ same residue
NOTCH2 p.Arg2003Ter Pathogenic/Likely pathogenic ★★ same condition
NOTCH2 p.Arg2400Ter Pathogenic ★★ same condition
NOTCH2 p.Gln2223Ter Pathogenic ★★ same condition
NOTCH2 p.Gln2263Ter Pathogenic ★★ same condition
NOTCH2 p.Gln2285Ter Pathogenic/Likely pathogenic ★★ same condition
NOTCH2 c.2753-8T>A Uncertain significance ★★ same condition
NOTCH2 c.5214-10A>G 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/notch2-p-asp813 (accessed [today's date]).

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