Is DPP10 p.Ile721Val (c.2161A>G) pathogenic?

DPP10 p.Ile721Val (c.2161A>G) is classified Uncertain significance in DPP10 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-16). AlphaMissense: likely benign (0.1522); Absent from gnomAD v4.1.

How common is DPP10 p.Ile721Val (c.2161A>G) in the general population?

DPP10 p.Ile721Val (c.2161A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DPP10 p.Ile721Val (c.2161A>G)?

AlphaMissense predicts likely benign (score 0.1522) — an in-silico prediction, not a clinical call.

DPP10 p.Ile721Val

c.2161A>G · rs2472901214 · VCV2289910

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1522 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1522	likely benign
REVEL	0.053	moderately benign-leaning
SaProt	LLR -7.75	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 6.8	GERP 0.54, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 103 kb · p 0.025 · regional, not allelic
Overall
CADD	19.26	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DPP10
Protein: p.Ile721Val
Coding: c.2161A>G
MANE Select: NM_020868
dbSNP: rs2472901214
Type: single nucleotide variant
Location: chr2:115836725 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB
Residue 721: a β-strand

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-ile721val (accessed [today's date]).

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