Is DPP10 p.Glu234Asp (c.702A>C) pathogenic?

DPP10 p.Glu234Asp (c.702A>C) is classified Benign in DPP10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-06-22). AlphaMissense: ambiguous (0.4278); Low-frequency (popmax 1.2%, afr).

How common is DPP10 p.Glu234Asp (c.702A>C) in the general population?

DPP10 p.Glu234Asp (c.702A>C) is low-frequency (popmax 1.2%, afr) (gnomAD).

What do computational predictors say about DPP10 p.Glu234Asp (c.702A>C)?

AlphaMissense predicts ambiguous (score 0.4278) — an in-silico prediction, not a clinical call.

DPP10 p.Glu234Asp

c.702A>C · rs78880257 · VCV712427

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4278 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.2%, afr)

Computational evidence

Protein change
AlphaMissense	0.4278	ambiguous
REVEL	0.638	indeterminate
SaProt	LLR -8.36	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.5	GERP -2.6, phastCons 1
Regional constraint	o/e 0.49	unconstrained · MANE · 50 kb · p 1.8e-06 · regional, not allelic
Overall
CADD	21.8	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 1.2% African / African-American · 898/74,976 alleles

Filtering AF 1.13% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.11%

Overall 0.0649% 1,047/1,613,074 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.2%	83
Admixed American	0.12%	833
Remaining individualsnot grpmax-eligible	0.104%	961
Middle Eastern	0.0662%	1,512
South Asian	0.0011%	91,052
European (non-Finnish)	0.000594%	168,469

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: DPP10
Protein: p.Glu234Asp
Coding: c.702A>C
MANE Select: NM_020868
dbSNP: rs78880257
Type: single nucleotide variant
Location: chr2:115739743 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB
Residue 234: an α-helix

Full DPP10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPP10 p.Glu234Gln Uncertain significance ★ ⚠ same residue
DPP10 p.Asp380= Benign ★★ same type
DPP10 p.Gly601Ser Benign ★★ ⚠ same type
DPP10 p.His130= Likely benign ★★ same type
DPP10 p.Leu575= Benign ★★ same type
DPP10 c.852+1G>T Uncertain significance ★ same type
DPP10 p.Ala112Ser Uncertain significance ★ ⚠ same type
DPP10 p.Ala455Val 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/dpp10-p-glu234asp (accessed [today's date]).

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