DNER p.Ser560=
c.1680C>T · rs200801433 · VCV743004
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.557%, sas)
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 -8.3 | GERP -3 |
| Overall | ||
| CADD | 0.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.557%
South Asian · 507/91,052 alleles
Filtering AF
0.517%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.501%
Overall
0.0355%
573/1,613,658 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.557% | 180 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| Middle Eastern | 0.0165% | 6,056 |
| African / African-American | 0.00533% | 18,758 |
| European (non-Finnish) | 0.00314% | 31,882 |
| East Asian | 0.00223% | 44,870 |
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
- DNER
- Protein
- p.Ser560=
- Coding
- c.1680C>T
- MANE Select
- NM_139072
- dbSNP
- rs200801433
- Type
- single nucleotide variant
- Location
- chr2:229407275 (GRCh38)
- Gene constraint
- LOEUF 0.561 · pLI 0.21 (gnomAD)
- Structure
- AlphaFold pLDDT 70.51
- Residue 560
- the egf-like 9 domain; the follistatin-like domain; a disulfide bond
Similar variants
- DNER c.586-10C>T Benign ★★ same type
- DNER p.Arg698= Benign ★★ same type
- DNER p.Pro180= Benign ★★ same type
- DNER p.Thr142Ile Benign ★★ ⚠ same type
- DNER p.Ala11Val Uncertain significance ★ ⚠ same type
- DNER p.Ala171Thr Uncertain significance ★ ⚠ same type
- DNER p.Ala205Thr Uncertain significance ★ ⚠ same type
- DNER p.Ala234Thr 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/dner-p-ser560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown