Is DPP10 p.Asn593Ser (c.1778A>G) pathogenic?

DPP10 p.Asn593Ser (c.1778A>G) is classified Uncertain significance in DPP10 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-12). AlphaMissense: likely benign (0.0779); Ultra-rare (popmax 0.0254%, afr).

How common is DPP10 p.Asn593Ser (c.1778A>G) in the general population?

DPP10 p.Asn593Ser (c.1778A>G) is ultra-rare (popmax 0.0254%, afr) (gnomAD).

What do computational predictors say about DPP10 p.Asn593Ser (c.1778A>G)?

AlphaMissense predicts likely benign (score 0.0779) — an in-silico prediction, not a clinical call.

DPP10 p.Asn593Ser

c.1778A>G · rs373895432 · VCV2365746

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0779 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0254%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0779	likely benign
REVEL	0.04	moderately benign-leaning
SaProt	LLR -7.91	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 6.8	GERP 0.69, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 103 kb · p 0.025 · regional, not allelic
Overall
CADD	17.47	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

Grpmax group 0.0254% African / African-American · 19/74,892 alleles

Filtering AF 0.0166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0137%

Overall 0.00242% 39/1,610,934 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0254%	3,942
Middle Eastern	0.0165%	6,072
Remaining individualsnot grpmax-eligible	0.0128%	7,791
South Asian	0.0011%	90,610
European (non-Finnish)	0.000849%	117,788

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.Asn593Ser
Coding: c.1778A>G
MANE Select: NM_020868
dbSNP: rs373895432
Type: single nucleotide variant
Location: chr2:115814870 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB
Residue 593: 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-asn593ser (accessed [today's date]).

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