Is DPP6 p.Ala5= (c.15C>T) pathogenic?

DPP6 p.Ala5= (c.15C>T) is classified Benign in DPP6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-04-18). Low-frequency (popmax 3.61%, eas); Associated with DPP6-related disorder.

What condition is associated with DPP6 p.Ala5= (c.15C>T)?

DPP6 p.Ala5= (c.15C>T) is associated with DPP6-related disorder (ClinVar).

How common is DPP6 p.Ala5= (c.15C>T) in the general population?

DPP6 p.Ala5= (c.15C>T) is low-frequency (popmax 3.61%, eas) (gnomAD).

DPP6 p.Ala5=

c.15C>T · VCV3350375

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 3.61%, eas)

Conditions

DPP6-related disorder

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 0.084	GERP 3.3, phastCons 0.76
Overall
CADD	10.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.61% East Asian · 1,618/44,846 alleles

Filtering AF 3.46% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.4%

Overall 0.114% 1,834/1,613,904 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	3.61%	28
Remaining individualsnot grpmax-eligible	0.136%	735
South Asian	0.127%	785
Middle Eastern	0.0165%	6,062
Admixed American	0.00333%	30,010
European (non-Finnish)	0.00102%	98,323

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.Ala5=
Coding: c.15C>T
MANE Select: NM_130797 · reported on NM_001364501
Type: single nucleotide variant
Location: chr7:153887698 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 87.41 · 8 PDB
Residue 5: the 'disordered' region

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

Disease context

DPP6-related disorder

Similar variants

DPP6 p.Ala5Val Uncertain significance ★ same residue
DPP6 c.1299+68G>A Uncertain significance ★ same condition
DPP6 c.244-1G>A Uncertain significance ★ same condition
DPP6 p.Glu139Lys Uncertain significance ⚠ same condition
DPP6 p.His267Leu Uncertain significance ⚠ same condition
DPP6 p.Tyr205Asn Uncertain significance ⚠ same condition
DPP6 c.1299+179C>G Likely benign same condition
DPP6 c.1299+18G>A Likely benign 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-ala5 (accessed [today's date]).

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