Is DPP9 p.Asp42= (c.126C>T) pathogenic?

DPP9 p.Asp42= (c.126C>T) is classified Likely benign in DPP9 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-06-01). Rare (popmax 0.156%, nfe).

How common is DPP9 p.Asp42= (c.126C>T) in the general population?

DPP9 p.Asp42= (c.126C>T) is rare (popmax 0.156%, nfe) (gnomAD).

DPP9 p.Asp42=

c.126C>T · VCV3777832

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.156%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.1	GERP -3
Overall
CADD	1.093	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.156% European (non-Finnish) · 1,806/1,155,762 alleles

Filtering AF 0.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.148%

Overall 0.133% 2,069/1,560,938 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.19%	526
European (non-Finnish)grpmax	0.156%	640
Remaining individualsnot grpmax-eligible	0.122%	819
South Asian	0.0685%	1,459
Admixed American	0.0298%	3,357
African / African-American	0.0135%	7,380
East Asian	0.00475%	21,060
Ashkenazi Jewishnot grpmax-eligible	0.00347%	28,816

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DPP9
Protein: p.Asp42=
Coding: c.126C>T
MANE Select: NM_139159
Type: single nucleotide variant
Location: chr19:4714268 (GRCh38)
Gene constraint: LOEUF 0.647 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.96 · 14 PDB
Residue 42: an α-helix

Full DPP9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPP9 p.Asp310Asn Uncertain significance ★★ ⚠ same type
DPP9 p.Lys509Arg Uncertain significance ★★ ⚠ same type
DPP9 p.Thr301Met Uncertain significance ★★ ⚠ same type
DPP9 p.Ala184Gly Benign/Likely benign ★★ same type
DPP9 p.Glu566Lys Benign/Likely benign ★★ ⚠ same type
DPP9 p.His83= Benign/Likely benign ★★ same type
DPP9 p.Pro322= Benign ★★ same type
DPP9 p.Ser236Asn 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/dpp9-p-asp42 (accessed [today's date]).

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