Is DPP3 p.Glu642Lys (c.1924G>A) pathogenic?

DPP3 p.Glu642Lys (c.1924G>A) is classified Benign in DPP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-19). AlphaMissense: likely benign (0.1512); Rare (popmax 0.919%, afr).

How common is DPP3 p.Glu642Lys (c.1924G>A) in the general population?

DPP3 p.Glu642Lys (c.1924G>A) is rare (popmax 0.919%, afr) (gnomAD).

What do computational predictors say about DPP3 p.Glu642Lys (c.1924G>A)?

AlphaMissense predicts likely benign (score 0.1512) — an in-silico prediction, not a clinical call.

DPP3 p.Glu642Lys

c.1924G>A · rs114407249 · VCV722850

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1512 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.919%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1512	likely benign
REVEL	0.129	moderately benign-leaning
SaProt	LLR -10.75	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.3	GERP 1.4, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 27 kb · p 1e-05 · regional, not allelic
Overall
CADD	23.0	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 0.919% African / African-American · 689/74,996 alleles

Filtering AF 0.862% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.839%

Overall 0.0504% 813/1,613,454 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.919%	109
Admixed American	0.108%	923
Remaining individualsnot grpmax-eligible	0.0736%	1,358
South Asian	0.0022%	45,500
European (non-Finnish)	0.000932%	107,256

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: DPP3
Protein: p.Glu642Lys
Coding: c.1924G>A
MANE Select: NM_130443
dbSNP: rs114407249
Type: single nucleotide variant
Location: chr11:66504657 (GRCh38)
Gene constraint: LOEUF 0.827 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.56 · 10 PDB
Residue 642: an α-helix

Full DPP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPP3 p.Arg76His Benign ★★ ⚠ same type
DPP3 p.Leu163Met Benign ★★ ⚠ same type
DPP3 p.Lys423= Benign ★★ same type
DPP3 p.Phe331= Benign ★★ same type
DPP3 p.Phe443= Benign ★★ same type
DPP3 p.Thr401= Benign ★★ same type
DPP3 c.573+1G>A Uncertain significance ★ same type
DPP3 p.Ala22Gly 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/dpp3-p-glu642lys (accessed [today's date]).

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