Is CTU2 p.Arg246= (c.736C>A) pathogenic?

CTU2 p.Arg246= (c.736C>A) is classified Likely benign in CTU2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-15). Absent from gnomAD v4.1; Associated with CTU2-related disorder.

What condition is associated with CTU2 p.Arg246= (c.736C>A)?

CTU2 p.Arg246= (c.736C>A) is associated with CTU2-related disorder (ClinVar).

How common is CTU2 p.Arg246= (c.736C>A) in the general population?

CTU2 p.Arg246= (c.736C>A) is absent from gnomAD v4.1 (gnomAD).

CTU2 p.Arg246=

c.736C>A · rs767710092 · VCV3049500

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,509,668)

Conditions

CTU2-related disorder

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 1.6	GERP -1.8, phastCons 1
Overall
CADD	11.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,509,668). 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: CTU2
Protein: p.Arg246=
Coding: c.736C>A
MANE Select: NM_001012759
dbSNP: rs767710092
Type: single nucleotide variant
Location: chr16:88712904 (GRCh38)
Gene constraint: LOEUF 1.535 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.27

Full CTU2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CTU2-related disorder

Similar variants

CTU2 p.Arg246Gln Uncertain significance ★ ⚠ same residue
CTU2 p.Arg246Trp Uncertain significance ★ ⚠ same residue
CTU2 p.Thr291= Pathogenic ★★ same condition
CTU2 p.Leu63Pro Conflicting classifications of pathogenicity ★ ⚠ same condition
CTU2 c.1097+5G>A Uncertain significance same condition
CTU2 c.1202-8G>A Likely benign same condition
CTU2 c.1353-4G>A Likely benign same condition
CTU2 c.1419+8C>T Likely benign 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/ctu2-p-arg246 (accessed [today's date]).

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