Is DCP2 p.Gln79Pro (c.236A>C) pathogenic?

DCP2 p.Gln79Pro (c.236A>C) is classified Uncertain significance in DCP2 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-02-22). AlphaMissense: likely benign (0.0795); Very rare (popmax 0.000593%, nfe).

How common is DCP2 p.Gln79Pro (c.236A>C) in the general population?

DCP2 p.Gln79Pro (c.236A>C) is very rare (popmax 0.000593%, nfe) (gnomAD).

What do computational predictors say about DCP2 p.Gln79Pro (c.236A>C)?

AlphaMissense predicts likely benign (score 0.0795) — an in-silico prediction, not a clinical call.

DCP2 p.Gln79Pro

c.236A>C · rs764907689 · VCV2466197

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0795 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000593%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0795	likely benign
REVEL	0.18	moderately benign-leaning
SaProt	LLR -12.16	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	Δ0.50	acceptor loss, 23 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 16 kb · p 0.92 · regional, not allelic
Overall
CADD	24.2	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 0.000593% European (non-Finnish) · 7/1,179,956 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000434% 7/1,613,972 alleles · very rare exomes 7/1,461,650 · genomes 0/152,322 · joint denominator

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.Gln79Pro
Coding: c.236A>C
MANE Select: NM_152624
dbSNP: rs764907689
Type: single nucleotide variant
Location: chr5:112992151 (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-gln79pro (accessed [today's date]).

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