Is DCP2 p.Gln52Lys (c.154C>A) pathogenic?

DCP2 p.Gln52Lys (c.154C>A) is classified Uncertain significance in DCP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-25). AlphaMissense: likely benign (0.2195); Ultra-rare (popmax 0.0521%, sas).

How common is DCP2 p.Gln52Lys (c.154C>A) in the general population?

DCP2 p.Gln52Lys (c.154C>A) is ultra-rare (popmax 0.0521%, sas) (gnomAD).

What do computational predictors say about DCP2 p.Gln52Lys (c.154C>A)?

AlphaMissense predicts likely benign (score 0.2195) — an in-silico prediction, not a clinical call.

DCP2 p.Gln52Lys

c.154C>A · rs747847949 · VCV3080578

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2195 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0521%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2195	likely benign
REVEL	0.199	benign-leaning
SaProt	LLR -6.64	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 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 16 kb · p 0.92 · regional, not allelic
Overall
CADD	24.5	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

Grpmax group 0.0521% South Asian · 47/90,196 alleles

Filtering AF 0.0402% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.036%

Overall 0.00823% 132/1,603,828 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0521%	1,919
Middle Eastern	0.0166%	6,042
European (non-Finnish)	0.00657%	15,223
African / African-American	0.00535%	18,706
Remaining individualsnot grpmax-eligible	0.00484%	20,641

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: DCP2
Protein: p.Gln52Lys
Coding: c.154C>A
MANE Select: NM_152624
dbSNP: rs747847949
Type: single nucleotide variant
Location: chr5:112985935 (GRCh38)
Gene constraint: LOEUF 0.793 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.25 · 33 PDB

Full DCP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCP2 p.Ala390Glu Uncertain significance ★ ⚠ same type
DCP2 p.Arg166Gln Uncertain significance ★ ⚠ same type
DCP2 p.Arg173Cys Uncertain significance ★ ⚠ same type
DCP2 p.Arg241Gln Uncertain significance ★ ⚠ same type
DCP2 p.Arg274Cys Uncertain significance ★ ⚠ same type
DCP2 p.Arg274His Uncertain significance ★ ⚠ same type
DCP2 p.Asn168Asp Uncertain significance ★ ⚠ same type
DCP2 p.Asn187Asp 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/dcp2-p-gln52lys (accessed [today's date]).

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