Is DPP10 p.Leu575= (c.1723C>T) pathogenic?

DPP10 p.Leu575= (c.1723C>T) is classified Benign in DPP10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-08-14). Common (popmax 6.06%, afr) — too common for a highly-penetrant pathogenic allele.

DPP10 p.Leu575=

Q: How common is DPP10 p.Leu575= (c.1723C>T) in the general population?

DPP10 p.Leu575= (c.1723C>T) is common (popmax 6.06%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1723C>T · rs113462911 · VCV782403

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 6.06%, afr) — 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 -0.06	GERP -2.9, phastCons 0.039
Overall
CADD	0.964	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.06% African / African-American · 4,504/74,380 alleles

Filtering AF 5.91% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.85%

Overall 0.355% 5,533/1,558,536 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.06%	17
Admixed American	0.687%	146
Middle Eastern	0.65%	154
Remaining individualsnot grpmax-eligible	0.511%	196
Ashkenazi Jewishnot grpmax-eligible	0.0809%	1,235
European (non-Finnish)	0.0217%	4,599
South Asian	0.00962%	10,394

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: DPP10
Protein: p.Leu575=
Coding: c.1723C>T
MANE Select: NM_020868
dbSNP: rs113462911
Type: single nucleotide variant
Location: chr2:115814815 (GRCh38)
Gene constraint: LOEUF 0.378 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 90.67 · 1 PDB

Full DPP10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPP10 p.Asp380= Benign ★★ same type
DPP10 p.Glu234Asp Benign ★★ ⚠ same type
DPP10 p.Gly601Ser Benign ★★ ⚠ same type
DPP10 p.His130= Likely benign ★★ same type
DPP10 c.852+1G>T Uncertain significance ★ same type
DPP10 p.Ala112Ser Uncertain significance ★ ⚠ same type
DPP10 p.Ala455Val Uncertain significance ★ ⚠ same type
DPP10 p.Ala726Ser 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/dpp10-p-leu575 (accessed [today's date]).

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