Is CTDSP2 p.Ser256= (c.768C>T) pathogenic?

CTDSP2 p.Ser256= (c.768C>T) is classified Likely benign in CTDSP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-11-06). Ultra-rare (popmax 0.01%, amr); Associated with CTDSP2-related disorder.

What condition is associated with CTDSP2 p.Ser256= (c.768C>T)?

CTDSP2 p.Ser256= (c.768C>T) is associated with CTDSP2-related disorder (ClinVar).

How common is CTDSP2 p.Ser256= (c.768C>T) in the general population?

CTDSP2 p.Ser256= (c.768C>T) is ultra-rare (popmax 0.01%, amr) (gnomAD).

CTDSP2 p.Ser256=

c.768C>T · rs762231419 · VCV3034914

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.01%, amr)

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 -4	GERP -4.5
Overall
CADD	6.009	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/59,992 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.000684% 10/1,461,758 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	9,999
East Asian	0.00668%	14,961
Remaining individualsnot grpmax-eligible	0.0016%	62,484

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CTDSP2
Protein: p.Ser256=
Coding: c.768C>T
MANE Select: NM_005730
dbSNP: rs762231419
Type: single nucleotide variant
Location: chr12:57823650 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.97 (gnomAD)
Structure: AlphaFold pLDDT 78.73 · 1 PDB

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.Ile249= 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-ser256 (accessed [today's date]).

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