Is DPP6 p.Cys735= (c.2205C>T) pathogenic?

DPP6 p.Cys735= (c.2205C>T) is classified Benign in DPP6 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-05-05). Common (popmax 19.9%, amr) — too common for a highly-penetrant pathogenic allele.

DPP6 p.Cys735=

Q: How common is DPP6 p.Cys735= (c.2205C>T) in the general population?

DPP6 p.Cys735= (c.2205C>T) is common (popmax 19.9%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2205C>T · rs3734959 · VCV1222704

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 19.9%, amr) — too common for a highly-penetrant pathogenic allele

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 -8.9	GERP -3.2
Overall
CADD	1.658	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 19.9% Admixed American · 11,506/57,768 alleles

Filtering AF 19.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 19.5%

Overall 1.2% 19,170/1,598,972 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	19.9%	5
East Asian	5.61%	18
Finnishnot grpmax-eligible	1.17%	86
Remaining individualsnot grpmax-eligible	1.04%	96
Ashkenazi Jewishnot grpmax-eligible	0.389%	257
African / African-American	0.301%	332
European (non-Finnish)	0.278%	359
South Asian	0.216%	463
Middle Eastern	0.132%	756

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: DPP6
Protein: p.Cys735=
Coding: c.2205C>T
MANE Select: NM_130797
dbSNP: rs3734959
Type: single nucleotide variant
Location: chr7:154885704 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 87.41 · 8 PDB
Residue 735: a disulfide bond; a β-strand

Full DPP6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPP6 p.Gly65Cys Uncertain significance ★★ ⚠ same type
DPP6 p.Gly65Val Uncertain significance ★★ ⚠ same type
DPP6 p.Lys223Arg Uncertain significance ★★ ⚠ same type
DPP6 p.Pro229Thr Uncertain significance ★★ ⚠ same type
DPP6 c.1261-188G>A Benign ★★ same type
DPP6 c.1261-48G>A Benign ★★ same type
DPP6 c.1299+147A>G Benign ★★ same type
DPP6 c.1299+200A>G 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/dpp6-p-cys735 (accessed [today's date]).

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