Is DPP6 p.Gly38= (c.114C>T) pathogenic?

DPP6 p.Gly38= (c.114C>T) is classified Benign in DPP6 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2021-05-04). Common (popmax 16%, sas) — too common for a highly-penetrant pathogenic allele.

DPP6 p.Gly38=

Q: How common is DPP6 p.Gly38= (c.114C>T) in the general population?

DPP6 p.Gly38= (c.114C>T) is common (popmax 16%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.114C>T · rs554552970 · VCV1247688

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 16%, sas) — 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 -0.03	GERP 2.8, phastCons 0.85
Overall
CADD	11.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 16% South Asian · 13,006/81,070 alleles

Filtering AF 15.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 15.7%

Overall 14.5% 211,146/1,453,984 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	16%	6
Middle Eastern	15.9%	6
European (non-Finnish)	15.8%	6
Amishnot grpmax-eligible	15.1%	7
Ashkenazi Jewishnot grpmax-eligible	14.3%	7
Finnishnot grpmax-eligible	13.3%	8
Remaining individualsnot grpmax-eligible	13.2%	8
Admixed American	8.21%	12
African / African-American	5.22%	19
East Asian	0.316%	317

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.Gly38=
Coding: c.114C>T
MANE Select: NM_130797
dbSNP: rs554552970
Type: single nucleotide variant
Location: chr7:154052934 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 87.41 · 8 PDB
Residue 38: the 'disordered' region

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-gly38 (accessed [today's date]).

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