Is CUX2 p.Pro724= (c.2172C>T) pathogenic?

CUX2 p.Pro724= (c.2172C>T) is classified Likely benign in CUX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-13). Absent from gnomAD v4.1.

How common is CUX2 p.Pro724= (c.2172C>T) in the general population?

CUX2 p.Pro724= (c.2172C>T) is absent from gnomAD v4.1 (gnomAD).

CUX2 p.Pro724=

c.2172C>T · VCV3336027

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 1,531,450)

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 -5.2	GERP -2.3
Overall
CADD	0.047	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,531,450). 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: CUX2
Protein: p.Pro724=
Coding: c.2172C>T
MANE Select: NM_015267
Type: single nucleotide variant
Location: chr12:111320181 (GRCh38)
Gene constraint: LOEUF 0.383 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 60.99 · 3 PDB
Residue 724: the 'disordered' region

Full CUX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CUX2 p.Glu590Lys Pathogenic/Likely pathogenic ★★ same type
CUX2 p.Ala302Ser Uncertain significance ★★ ⚠ same type
CUX2 p.Ala336Thr Uncertain significance ★★ ⚠ same type
CUX2 p.Ala544Val Uncertain significance ★★ ⚠ same type
CUX2 p.Arg312Gln Uncertain significance ★★ ⚠ same type
CUX2 p.Arg599Ser Uncertain significance ★★ ⚠ same type
CUX2 p.Arg701His Uncertain significance ★★ ⚠ same type
CUX2 p.Arg903His 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/cux2-p-pro724 (accessed [today's date]).

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