Is DPP10 p.Gln752Lys (c.2254C>A) pathogenic?

DPP10 p.Gln752Lys (c.2254C>A) is classified Likely benign in DPP10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-04-14). AlphaMissense: likely pathogenic (0.6837); Rare (popmax 0.629%, nfe); Associated with DPP10-related disorder.

What condition is associated with DPP10 p.Gln752Lys (c.2254C>A)?

DPP10 p.Gln752Lys (c.2254C>A) is associated with DPP10-related disorder (ClinVar).

How common is DPP10 p.Gln752Lys (c.2254C>A) in the general population?

DPP10 p.Gln752Lys (c.2254C>A) is rare (popmax 0.629%, nfe) (gnomAD).

What do computational predictors say about DPP10 p.Gln752Lys (c.2254C>A)?

AlphaMissense predicts likely pathogenic (score 0.6837) — an in-silico prediction, not a clinical call.

DPP10 p.Gln752Lys

c.2254C>A · rs146482002 · VCV3037826

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6837 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.629%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

DPP10-related disorder

Computational evidence

Protein change
AlphaMissense	0.6837	likely pathogenic
REVEL	0.363	indeterminate
SaProt	LLR -10.55	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.4	GERP 1.8, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 103 kb · p 0.025 · regional, not allelic
Overall
CADD	32.0	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 0.629% European (non-Finnish) · 7,407/1,177,680 alleles

Filtering AF 0.617% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.612%

Overall 0.52% 8,377/1,609,792 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.629%	159
Admixed American	0.515%	194
Remaining individualsnot grpmax-eligible	0.425%	235
African / African-American	0.172%	580
South Asian	0.163%	612
Ashkenazi Jewishnot grpmax-eligible	0.159%	628
Middle Eastern	0.116%	859
Finnishnot grpmax-eligible	0.105%	953

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.Gln752Lys
Coding: c.2254C>A
MANE Select: NM_020868
dbSNP: rs146482002
Type: single nucleotide variant
Location: chr2:115840821 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB
Residue 752: a β-strand

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.Lys625Arg 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-gln752lys (accessed [today's date]).

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