Is DPP7 p.Arg478Cys (c.1432C>T) pathogenic?

DPP7 p.Arg478Cys (c.1432C>T) is classified Uncertain significance in DPP7 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-09). AlphaMissense: likely benign (0.2233); Rare (popmax 0.609%, mid).

How common is DPP7 p.Arg478Cys (c.1432C>T) in the general population?

DPP7 p.Arg478Cys (c.1432C>T) is rare (popmax 0.609%, mid) (gnomAD).

What do computational predictors say about DPP7 p.Arg478Cys (c.1432C>T)?

AlphaMissense predicts likely benign (score 0.2233) — an in-silico prediction, not a clinical call.

DPP7 p.Arg478Cys

c.1432C>T · rs144785203 · VCV2397067

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2233 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.609%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2233	likely benign
REVEL	0.045	moderately benign-leaning
SaProt	LLR -9.95	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.59	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP -0.26	GERP -2.6
Regional constraint	o/e 1.17	unconstrained · MANE · 3,355 bp · p 5.6e-05 · regional, not allelic
Overall
CADD	9.517	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 0.609% Middle Eastern · 28/4,594 alleles

Filtering AF 0.433% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.374%

Overall 0.0508% 818/1,608,972 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.609%	164
European (non-Finnish)	0.0589%	1,698
Remaining individualsnot grpmax-eligible	0.0482%	2,077
Admixed American	0.04%	2,500
South Asian	0.0264%	3,792
African / African-American	0.016%	6,248
Finnishnot grpmax-eligible	0.00823%	12,153

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: DPP7
Protein: p.Arg478Cys
Coding: c.1432C>T
MANE Select: NM_013379
dbSNP: rs144785203
Type: single nucleotide variant
Location: chr9:137110695 (GRCh38)
Gene constraint: LOEUF 1.707 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.44 · 3 PDB

Full DPP7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPP7 p.Arg478His Uncertain significance ★ ⚠ same residue
DPP7 p.Arg17= Likely benign ★★ same type
DPP7 c.322-1G>T Uncertain significance ★ same type
DPP7 p.Ala118Gly Uncertain significance ★ ⚠ same type
DPP7 p.Ala118Val Uncertain significance ★ ⚠ same type
DPP7 p.Ala136Val Uncertain significance ★ ⚠ same type
DPP7 p.Ala139Gly Uncertain significance ★ ⚠ same type
DPP7 p.Ala13Val 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/dpp7-p-arg478cys (accessed [today's date]).

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