Is CTU2 p.Ala403fs (c.1206dup) pathogenic?

CTU2 p.Ala403fs (c.1206dup) is classified Pathogenic in CTU2 (ClinVar, Single submitter, 1 submitter). Absent from gnomAD; Associated with microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome.

How common is CTU2 p.Ala403fs (c.1206dup) in the general population?

CTU2 p.Ala403fs (c.1206dup) is absent from gnomAD (gnomAD).

CTU2 p.Ala403fs

Q: What condition is associated with CTU2 p.Ala403fs (c.1206dup)?

CTU2 p.Ala403fs (c.1206dup) is associated with microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (ClinVar).

c.1206dup · rs1597434884 · VCV635409

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 12 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.4	GERP 2.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Ala403fs
Coding: c.1206dup
MANE Select: NM_001012759
dbSNP: rs1597434884
Type: Duplication
Location: chr16:88714590 (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

microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CTU2 p.Ala403Val Uncertain significance ★ ⚠ same residue
CTU2 c.1420-1G>A Likely pathogenic ★★ same condition
CTU2 c.282+5G>A Pathogenic ★★ same condition
CTU2 p.Gln243Ter Pathogenic/Likely pathogenic ★★ same condition
CTU2 p.Thr291= Pathogenic ★★ same condition
CTU2 p.Gln416Ter Uncertain significance ★★ same condition
CTU2 c.1006-26A>G Benign ★★ same condition
CTU2 c.1097+6_1097+11del 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-ala403fs (accessed [today's date]).

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