Is DCTPP1 p.Pro115Arg (c.344C>G) pathogenic?

DCTPP1 p.Pro115Arg (c.344C>G) is classified Uncertain significance in DCTPP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-30). AlphaMissense: likely pathogenic (0.8076); Absent from gnomAD v4.1.

How common is DCTPP1 p.Pro115Arg (c.344C>G) in the general population?

DCTPP1 p.Pro115Arg (c.344C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCTPP1 p.Pro115Arg (c.344C>G)?

AlphaMissense predicts likely pathogenic (score 0.8076) — an in-silico prediction, not a clinical call.

DCTPP1 p.Pro115Arg

c.344C>G · VCV4658848

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8076 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8076	likely pathogenic
REVEL	0.287	benign-leaning
SaProt	LLR -8.16	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.7	GERP 2, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 5,744 bp · p 0.97 · regional, not allelic
Overall
CADD	24.6	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: DCTPP1
Protein: p.Pro115Arg
Coding: c.344C>G
MANE Select: NM_024096
Type: single nucleotide variant
Location: chr16:30424402 (GRCh38)
Gene constraint: LOEUF 1.458 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.40 · 5 PDB
Residue 115: an α-helix

Full DCTPP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCTPP1 p.Pro115Ala Uncertain significance ★ ⚠ same residue
DCTPP1 p.Pro115Leu Uncertain significance ★ ⚠ same residue
DCTPP1 p.Ala18Pro Uncertain significance ★ ⚠ same type
DCTPP1 p.Arg109Cys Uncertain significance ★ ⚠ same type
DCTPP1 p.Arg111Cys Uncertain significance ★ ⚠ same type
DCTPP1 p.Arg126Trp Uncertain significance ★ ⚠ same type
DCTPP1 p.Arg135Cys Uncertain significance ★ ⚠ same type
DCTPP1 p.Arg135His 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/dctpp1-p-pro115arg (accessed [today's date]).

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