Is DPP6 p.Gln271= (c.813G>A) pathogenic?

DPP6 p.Gln271= (c.813G>A) is classified Benign in DPP6 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2021-08-11). Common (popmax 6.6%, afr) — too common for a highly-penetrant pathogenic allele; Associated with intellectual disability, autosomal dominant 33.

What condition is associated with DPP6 p.Gln271= (c.813G>A)?

DPP6 p.Gln271= (c.813G>A) is associated with intellectual disability, autosomal dominant 33, ventricular fibrillation, paroxysmal familial, 2 (ClinVar).

DPP6 p.Gln271=

Q: How common is DPP6 p.Gln271= (c.813G>A) in the general population?

DPP6 p.Gln271= (c.813G>A) is common (popmax 6.6%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.813G>A · rs61736427 · VCV1297169

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 6.6%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

intellectual disability, autosomal dominant 33

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 4.7	GERP 1.4, phastCons 1
Overall
CADD	8.856	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.6% African / African-American · 4,951/74,990 alleles

Filtering AF 6.45% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.39%

Overall 0.471% 7,599/1,613,808 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.6%	15
South Asian	1.47%	68
Middle Eastern	0.742%	135
Remaining individualsnot grpmax-eligible	0.696%	144
Ashkenazi Jewishnot grpmax-eligible	0.442%	226
Admixed American	0.397%	252
East Asian	0.388%	258
European (non-Finnish)	0.0247%	4,054

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.Gln271=
Coding: c.813G>A
MANE Select: NM_130797
dbSNP: rs61736427
Type: single nucleotide variant
Location: chr7:154727817 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 87.41 · 8 PDB

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

Disease context

intellectual disability, autosomal dominant 33 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ventricular fibrillation, paroxysmal familial, 2

Similar variants

DPP6 p.Lys223Arg Uncertain significance ★★ ⚠ same condition
DPP6 p.Pro229Thr Uncertain significance ★★ ⚠ same condition
DPP6 p.Lys241= Benign ★★ same condition
DPP6 p.Arg775Ter Likely pathogenic ★ same condition
DPP6 p.Tyr205Ter Likely pathogenic ★ same condition
DPP6 c.1667-4A>G Uncertain significance ★ same condition
DPP6 c.2304+2T>C Uncertain significance ★ same condition
DPP6 c.457+3G>A Uncertain significance ★ same condition

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-gln271 (accessed [today's date]).

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