DPP10 p.Ser64=
c.192G>T · rs201248540 · VCV733622
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0669%, afr)
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 1.5 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 6.408 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0669%
African / African-American · 50/74,758 alleles
Filtering AF
0.0521%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0468%
Overall
0.00335%
54/1,610,364 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0669% | 1,495 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,174 |
| Admixed American | 0.00168% | 59,548 |
| European (non-Finnish) | 8.49e-05% | 1,178,410 |
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.Ser64=
- Coding
- c.192G>T
- MANE Select
- NM_020868
- dbSNP
- rs201248540
- Type
- single nucleotide variant
- Location
- chr2:115343833 (GRCh38)
- Gene constraint
- LOEUF 0.378 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.67 · 1 PDB
Similar variants
- DPP10 p.Ser64Leu Uncertain significance ★ ⚠ same residue
- 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 p.Leu575= Benign ★★ same type
- DPP10 c.852+1G>T Uncertain significance ★ same type
- DPP10 p.Ala112Ser 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-ser64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown