Is CTDSP2 p.Ile249= (c.747C>A) pathogenic?

CTDSP2 p.Ile249= (c.747C>A) is classified Likely benign in CTDSP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-11-06). Absent from gnomAD v4.1; Associated with CTDSP2-related disorder.

What condition is associated with CTDSP2 p.Ile249= (c.747C>A)?

CTDSP2 p.Ile249= (c.747C>A) is associated with CTDSP2-related disorder (ClinVar).

How common is CTDSP2 p.Ile249= (c.747C>A) in the general population?

CTDSP2 p.Ile249= (c.747C>A) is absent from gnomAD v4.1 (gnomAD).

CTDSP2 p.Ile249=

c.747C>A · rs752232234 · VCV3051125

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CTDSP2-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 2.2	GERP -1.1, phastCons 1
Overall
CADD	8.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CTDSP2
Protein: p.Ile249=
Coding: c.747C>A
MANE Select: NM_005730
dbSNP: rs752232234
Type: single nucleotide variant
Location: chr12:57823671 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.97 (gnomAD)
Structure: AlphaFold pLDDT 78.73 · 1 PDB
Residue 249: the fcp1 homology domain; an α-helix

Full CTDSP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CTDSP2-related disorder

Similar variants

CTDSP2 p.Gly207= Likely benign same condition
CTDSP2 p.Ser256= Likely benign same condition
CTDSP2 p.Tyr262= Likely benign same condition
CTDSP2 p.Ala66Glu Uncertain significance ★ ⚠ same type
CTDSP2 p.Arg179Trp Uncertain significance ★ ⚠ same type
CTDSP2 p.Arg184Gln Uncertain significance ★ ⚠ same type
CTDSP2 p.Arg46Cys Uncertain significance ★ ⚠ same type
CTDSP2 p.Arg46Gly 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/ctdsp2-p-ile249 (accessed [today's date]).

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