Is DCP1A p.Val331Asp (c.992T>A) pathogenic?

DCP1A p.Val331Asp (c.992T>A) is classified Uncertain significance in DCP1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-05). AlphaMissense: likely benign (0.1498); Ultra-rare (popmax 0.0147%, afr).

How common is DCP1A p.Val331Asp (c.992T>A) in the general population?

DCP1A p.Val331Asp (c.992T>A) is ultra-rare (popmax 0.0147%, afr) (gnomAD).

What do computational predictors say about DCP1A p.Val331Asp (c.992T>A)?

AlphaMissense predicts likely benign (score 0.1498) — an in-silico prediction, not a clinical call.

DCP1A p.Val331Asp

c.992T>A · rs782753531 · VCV3080566

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1498 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0147%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1498	likely benign
SaProt	LLR -8.06	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP -0.85, phastCons 0.86
Regional constraint	o/e 0.89	unconstrained · MANE · 32 kb · p 0.013 · regional, not allelic
Overall
CADD	20.9	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; SaProt is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0147% African / African-American · 11/74,892 alleles

Filtering AF 0.00816% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00633%

Overall 0.00192% 31/1,613,804 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0147%	6,808
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606
Admixed American	0.00333%	29,990
European (non-Finnish)	0.00144%	69,405

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: DCP1A
Protein: p.Val331Asp
Coding: c.992T>A
MANE Select: NM_018403
dbSNP: rs782753531
Type: single nucleotide variant
Location: chr3:53292460 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 59.22 · 2 PDB

Full DCP1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCP1A p.Ala447Val Benign ★★ same type
DCP1A p.Ala210Val Uncertain significance ★ ⚠ same type
DCP1A p.Ala268Thr Uncertain significance ★ ⚠ same type
DCP1A p.Ala344Ser Uncertain significance ★ ⚠ same type
DCP1A p.Ala3Val Uncertain significance ★ ⚠ same type
DCP1A p.Ala443Thr Uncertain significance ★ ⚠ same type
DCP1A p.Ala444Gly Uncertain significance ★ ⚠ same type
DCP1A p.Ala458Thr 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/dcp1a-p-val331asp (accessed [today's date]).

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