Is DCD p.Pro28Arg (c.83C>G) pathogenic?

DCD p.Pro28Arg (c.83C>G) is classified Uncertain significance in DCD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-22). AlphaMissense: likely benign (0.1146); Absent from gnomAD v4.1.

How common is DCD p.Pro28Arg (c.83C>G) in the general population?

DCD p.Pro28Arg (c.83C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DCD p.Pro28Arg (c.83C>G)?

AlphaMissense predicts likely benign (score 0.1146) — an in-silico prediction, not a clinical call.

DCD p.Pro28Arg

c.83C>G · VCV3838502

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1146 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1146	likely benign
REVEL	0.065	moderately benign-leaning
SaProt	LLR -7.51	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.18	GERP -2.1
Regional constraint	o/e 1.04	unconstrained · MANE · 3,587 bp · p 0.63 · regional, not allelic
Overall
CADD	15.66	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: DCD
Protein: p.Pro28Arg
Coding: c.83C>G
MANE Select: NM_053283
Type: single nucleotide variant
Location: chr12:54647135 (GRCh38)
Gene constraint: LOEUF 1.809 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.88 · 4 PDB
Residue 28: the 'disordered' region

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

Similar variants

DCD p.Asp71Asn Benign ★★ ⚠ same type
DCD p.Asn32Lys Uncertain significance ★ ⚠ same type
DCD p.Asn32Ser Uncertain significance ★ ⚠ same type
DCD p.Asp101Glu Uncertain significance ★ ⚠ same type
DCD p.Glu89Lys Uncertain significance ★ ⚠ same type
DCD p.Glu92Gly Uncertain significance ★ ⚠ same type
DCD p.Gly46Val Uncertain significance ★ ⚠ same type
DCD p.Gly81Arg 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/dcd-p-pro28arg (accessed [today's date]).

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