Is DPP10 p.Arg212Gln (c.635G>A) pathogenic?

DPP10 p.Arg212Gln (c.635G>A) is classified Uncertain significance in DPP10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-06). AlphaMissense: likely pathogenic (0.706); Very rare (popmax 0.00223%, sas).

How common is DPP10 p.Arg212Gln (c.635G>A) in the general population?

DPP10 p.Arg212Gln (c.635G>A) is very rare (popmax 0.00223%, sas) (gnomAD).

What do computational predictors say about DPP10 p.Arg212Gln (c.635G>A)?

AlphaMissense predicts likely pathogenic (score 0.706) — an in-silico prediction, not a clinical call.

DPP10 p.Arg212Gln

c.635G>A · VCV3504920

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.706 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.706	likely pathogenic
REVEL	0.385	indeterminate
SaProt	LLR -8.27	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.5, phastCons 1
Regional constraint	o/e 0.49	unconstrained · MANE · 50 kb · p 1.8e-06 · regional, not allelic
Overall
CADD	33.0	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 0.00223% South Asian · 2/89,764 alleles

Filtering AF 0.00043% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000313%

Overall 0.00081% 13/1,605,634 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00223%	44,882
Remaining individualsnot grpmax-eligible	0.00161%	62,122
European (non-Finnish)	0.00085%	117,643

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.Arg212Gln
Coding: c.635G>A
MANE Select: NM_020868
Type: single nucleotide variant
Location: chr2:115727874 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB

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-arg212gln (accessed [today's date]).

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