DPT p.Ser34=
c.102C>T · rs550327408 · VCV730477
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -3.9 | GERP -2 |
| Overall | ||
| CADD | 5.956 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00186%
30/1,614,196 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| European (non-Finnish) | 0.00212% | 47,201 |
| Admixed American | 0.00167% | 60,018 |
| African / African-American | 0.00133% | 75,052 |
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
- DPT
- Protein
- p.Ser34=
- Coding
- c.102C>T
- MANE Select
- NM_001937
- dbSNP
- rs550327408
- Type
- single nucleotide variant
- Location
- chr1:168729073 (GRCh38)
- Gene constraint
- LOEUF 0.963 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.21
- Residue 34
- the '2 x 53-55 aa tandem repeats' region
Similar variants
- DPT p.Ser34Arg Uncertain significance ★ ⚠ same residue
- DPT p.Ala58= Benign ★★ same type
- DPT p.Phe130= Likely benign ★★ same type
- DPT p.Ser83Ile Likely benign ★★ same type
- DPT p.Tyr194= Benign ★★ same type
- DPT p.Val201Ile Benign ★★ same type
- DPT p.Arg126Gln Uncertain significance ★ ⚠ same type
- DPT p.Arg134Cys 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/dpt-p-ser34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown