Is DPP9 p.Thr329Met (c.986C>T) pathogenic?

DPP9 p.Thr329Met (c.986C>T) is classified Benign in DPP9 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-06-14). AlphaMissense: likely benign (0.0861); Low-frequency (popmax 3.45%, amr).

How common is DPP9 p.Thr329Met (c.986C>T) in the general population?

DPP9 p.Thr329Met (c.986C>T) is low-frequency (popmax 3.45%, amr) (gnomAD).

What do computational predictors say about DPP9 p.Thr329Met (c.986C>T)?

AlphaMissense predicts likely benign (score 0.0861) — an in-silico prediction, not a clinical call.

DPP9 p.Thr329Met

c.986C>T · rs148904342 · VCV769947

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0861 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 3.45%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0861	likely benign
REVEL	0.196	benign-leaning
SaProt	LLR -7.54	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 8.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 34 kb · p 0.00027 · regional, not allelic
Overall
CADD	26.8	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM T300M vs ClinVar T329M) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.45% Admixed American · 2,069/60,004 alleles

Filtering AF 3.32% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.27%

Overall 0.139% 2,242/1,613,926 alleles · low-frequency

Ancestry group	Frequency	1 in
Admixed Americangrpmax	3.45%	29
Remaining individualsnot grpmax-eligible	0.102%	976
African / African-American	0.028%	3,573
European (non-Finnish)	0.00737%	13,561
South Asian	0.0011%	91,086

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.Thr329Met
Coding: c.986C>T
MANE Select: NM_139159
dbSNP: rs148904342
Type: single nucleotide variant
Location: chr19:4702053 (GRCh38)
Gene constraint: LOEUF 0.647 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.96 · 14 PDB
Residue 329: a UniProt-annotated variant site (in hatis; likely pathogenic)

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-thr329met (accessed [today's date]).

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