Is DPP10 p.Leu609Arg (c.1826T>G) pathogenic?

DPP10 p.Leu609Arg (c.1826T>G) is classified Benign in DPP10 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-13). AlphaMissense: likely benign (0.1451); Rare (popmax 0.964%, afr).

How common is DPP10 p.Leu609Arg (c.1826T>G) in the general population?

DPP10 p.Leu609Arg (c.1826T>G) is rare (popmax 0.964%, afr) (gnomAD).

What do computational predictors say about DPP10 p.Leu609Arg (c.1826T>G)?

AlphaMissense predicts likely benign (score 0.1451) — an in-silico prediction, not a clinical call.

DPP10 p.Leu609Arg

c.1826T>G · rs147125069 · VCV734587

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1451 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.964%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1451	likely benign
REVEL	0.12	moderately benign-leaning
SaProt	LLR -1.42	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 7.6	GERP -1.7, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 103 kb · p 0.025 · regional, not allelic
Overall
CADD	26.3	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 0.964% African / African-American · 723/75,038 alleles

Filtering AF 0.905% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.882%

Overall 0.0507% 818/1,612,976 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.964%	104
Middle Eastern	0.0991%	1,009
Remaining individualsnot grpmax-eligible	0.0544%	1,837
Admixed American	0.0333%	3,001
South Asian	0.0044%	22,735
European (non-Finnish)	0.00263%	38,037

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.Leu609Arg
Coding: c.1826T>G
MANE Select: NM_020868
dbSNP: rs147125069
Type: single nucleotide variant
Location: chr2:115814918 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB
Residue 609: a turn

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

Similar variants

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
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-leu609arg (accessed [today's date]).

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