Is DCP1B p.Pro567= (c.1701G>A) pathogenic?

DCP1B p.Pro567= (c.1701G>A) is classified Benign in DCP1B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). Common (popmax 9.28%, afr) — too common for a highly-penetrant pathogenic allele.

DCP1B p.Pro567=

Q: How common is DCP1B p.Pro567= (c.1701G>A) in the general population?

DCP1B p.Pro567= (c.1701G>A) is common (popmax 9.28%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1701G>A · rs16928961 · VCV776685

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 9.28%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7.8	GERP -2.8
Overall
CADD	0.483	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.28% African / African-American · 6,959/75,002 alleles

Filtering AF 9.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.02%

Overall 0.487% 7,857/1,614,056 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	9.28%	11
Admixed American	0.643%	155
Remaining individualsnot grpmax-eligible	0.614%	163
Middle Eastern	0.33%	303
South Asian	0.022%	4,554
European (non-Finnish)	0.00729%	13,721
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606
East Asian	0.00223%	44,884

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.Pro567=
Coding: c.1701G>A
MANE Select: NM_152640
dbSNP: rs16928961
Type: single nucleotide variant
Location: chr12:1949158 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.19

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

Similar variants

DCP1B p.Ser301Thr Benign ★★ same type
DCP1B p.Ala302Thr Uncertain significance ★ ⚠ same type
DCP1B p.Ala387Val Uncertain significance ★ ⚠ same type
DCP1B p.Ala475Thr Uncertain significance ★ ⚠ same type
DCP1B p.Ala520Val Uncertain significance ★ ⚠ same type
DCP1B p.Ala585Thr Uncertain significance ★ ⚠ same type
DCP1B p.Ala612Thr Uncertain significance ★ ⚠ same type
DCP1B p.Arg314Gln 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/dcp1b-p-pro567 (accessed [today's date]).

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