Is CPTP p.Ser35Thr (c.104G>C) pathogenic?

CPTP p.Ser35Thr (c.104G>C) is classified Uncertain significance in CPTP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-25). AlphaMissense: ambiguous (0.3541); Absent from gnomAD v4.1.

How common is CPTP p.Ser35Thr (c.104G>C) in the general population?

CPTP p.Ser35Thr (c.104G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CPTP p.Ser35Thr (c.104G>C)?

AlphaMissense predicts ambiguous (score 0.3541) — an in-silico prediction, not a clinical call.

CPTP p.Ser35Thr

c.104G>C · VCV4006449

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3541 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3541	ambiguous
REVEL	0.126	moderately benign-leaning
SaProt	LLR -8.46	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.2, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 849 bp · p 0.1 · regional, not allelic
Overall
CADD	23.9	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

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: CPTP
Protein: p.Ser35Thr
Coding: c.104G>C
MANE Select: NM_001029885
Type: single nucleotide variant
Location: chr1:1327014 (GRCh38)
Gene constraint: LOEUF 1.748 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.93 · 6 PDB
Residue 35: an α-helix

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

Similar variants

CPTP p.Ala132Thr Uncertain significance ★ ⚠ same type
CPTP p.Arg106Gln Uncertain significance ★ ⚠ same type
CPTP p.Arg106Gly Uncertain significance ★ same type
CPTP p.Arg106Trp Uncertain significance ★ ⚠ same type
CPTP p.Arg110Cys Uncertain significance ★ ⚠ same type
CPTP p.Arg110His Uncertain significance ★ ⚠ same type
CPTP p.Arg126Cys Uncertain significance ★ ⚠ same type
CPTP p.Arg133Cys 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/cptp-p-ser35thr (accessed [today's date]).

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