Is DCP1B p.Ala3Pro (c.7G>C) pathogenic?

DCP1B p.Ala3Pro (c.7G>C) is classified Uncertain significance in DCP1B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-26). AlphaMissense: ambiguous (0.4793); Ultra-rare (popmax 0.0112%, eas).

How common is DCP1B p.Ala3Pro (c.7G>C) in the general population?

DCP1B p.Ala3Pro (c.7G>C) is ultra-rare (popmax 0.0112%, eas) (gnomAD).

What do computational predictors say about DCP1B p.Ala3Pro (c.7G>C)?

AlphaMissense predicts ambiguous (score 0.4793) — an in-silico prediction, not a clinical call.

DCP1B p.Ala3Pro

c.7G>C · rs539589278 · VCV3080575

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4793 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0112%, eas)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4793	ambiguous
REVEL	0.16	moderately benign-leaning
SaProt	LLR -9.86	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.51	GERP 0.88, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 58 kb · p 0.25 · regional, not allelic
Overall
CADD	22.4	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

Grpmax group 0.0112% East Asian · 5/44,830 alleles

Filtering AF 0.00435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00276%

Overall 0.000373% 6/1,608,994 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0112%	8,966
European (non-Finnish)	8.49e-05%	1,178,105

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: DCP1B
Protein: p.Ala3Pro
Coding: c.7G>C
MANE Select: NM_000719 · reported on NM_152640
dbSNP: rs539589278
Type: single nucleotide variant
Location: chr12:2004425 (GRCh38)

Full DCP1B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/dcp1b-p-ala3pro (accessed [today's date]).

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