Is DPP10 p.Lys625Arg (c.1874A>G) pathogenic?

DPP10 p.Lys625Arg (c.1874A>G) is classified Likely benign in DPP10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-04-09). AlphaMissense: likely benign (0.0816); Rare (popmax 0.244%, nfe); Associated with DPP10-related disorder.

What condition is associated with DPP10 p.Lys625Arg (c.1874A>G)?

DPP10 p.Lys625Arg (c.1874A>G) is associated with DPP10-related disorder (ClinVar).

How common is DPP10 p.Lys625Arg (c.1874A>G) in the general population?

DPP10 p.Lys625Arg (c.1874A>G) is rare (popmax 0.244%, nfe) (gnomAD).

What do computational predictors say about DPP10 p.Lys625Arg (c.1874A>G)?

AlphaMissense predicts likely benign (score 0.0816) — an in-silico prediction, not a clinical call.

DPP10 p.Lys625Arg

c.1874A>G · rs142359009 · VCV3044583

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0816 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.244%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DPP10-related disorder

Computational evidence

Protein change
AlphaMissense	0.0816	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -7.06	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 0.71, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 103 kb · p 0.025 · regional, not allelic
Overall
CADD	22.6	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 0.244% European (non-Finnish) · 2,872/1,174,954 alleles

Filtering AF 0.237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.234%

Overall 0.197% 3,171/1,607,642 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	1.21%	83
European (non-Finnish)grpmax	0.244%	409
Remaining individualsnot grpmax-eligible	0.241%	415
Finnishnot grpmax-eligible	0.0799%	1,252
Admixed American	0.045%	2,221
South Asian	0.0409%	2,446
African / African-American	0.0293%	3,409
Middle Eastern	0.0166%	6,030

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Lys625Arg
Coding: c.1874A>G
MANE Select: NM_020868
dbSNP: rs142359009
Type: single nucleotide variant
Location: chr2:115814966 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB
Residue 625: an α-helix

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

Disease context

DPP10-related disorder

Similar variants

DPP10 p.Ile54Met Uncertain significance ⚠ same condition
DPP10 c.61-147288C>T Likely benign same condition
DPP10 c.61-147289G>T Likely benign same condition
DPP10 p.Gln752Lys Likely benign same condition
DPP10 p.Asp380= Benign ★★ same type
DPP10 p.Glu234Asp Benign ★★ same type
DPP10 p.Gly601Ser Benign ★★ same type
DPP10 p.His130= Likely benign ★★ 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-lys625arg (accessed [today's date]).

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