Is CTU1 p.Arg283Pro (c.848G>C) pathogenic?

CTU1 p.Arg283Pro (c.848G>C) is classified Likely benign in CTU1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-03). AlphaMissense: likely benign (0.0592); Absent from gnomAD v4.1.

How common is CTU1 p.Arg283Pro (c.848G>C) in the general population?

CTU1 p.Arg283Pro (c.848G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTU1 p.Arg283Pro (c.848G>C)?

AlphaMissense predicts likely benign (score 0.0592) — an in-silico prediction, not a clinical call.

CTU1 p.Arg283Pro

c.848G>C · rs2514420305 · VCV3078877

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0592 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,041,636)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0592	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -0.81	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP -1.5, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 5,790 bp · p 0.053 · regional, not allelic
Overall
CADD	15.43	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

No allele count reported in gnomAD v4.1 (AN 1,041,636). 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: CTU1
Protein: p.Arg283Pro
Coding: c.848G>C
MANE Select: NM_145232
dbSNP: rs2514420305
Type: single nucleotide variant
Location: chr19:51098800 (GRCh38)
Gene constraint: LOEUF 1.978 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.51

Full CTU1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTU1 p.Ala131Gly Uncertain significance ★ ⚠ same type
CTU1 p.Ala131Ser Uncertain significance ★ ⚠ same type
CTU1 p.Ala131Val Uncertain significance ★ ⚠ same type
CTU1 p.Ala154Gly Uncertain significance ★ ⚠ same type
CTU1 p.Ala154Pro Uncertain significance ★ ⚠ same type
CTU1 p.Ala206Thr Uncertain significance ★ ⚠ same type
CTU1 p.Ala240Thr Uncertain significance ★ ⚠ same type
CTU1 p.Ala276Val 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/ctu1-p-arg283pro (accessed [today's date]).

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