DNER p.Cys434=
c.1302C>T · rs140576705 · VCV734588
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.52%, 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 -5.7 | GERP -3.7 |
| Overall | ||
| CADD | 2.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.52%
African / African-American · 1,138/75,038 alleles
Filtering AF
1.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.41%
Overall
0.107%
1,732/1,614,160 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.52% | 66 |
| Middle Eastern | 0.462% | 216 |
| Remaining individualsnot grpmax-eligible | 0.187% | 534 |
| Finnishnot grpmax-eligible | 0.183% | 547 |
| Admixed American | 0.165% | 606 |
| European (non-Finnish) | 0.019% | 5,268 |
| South Asian | 0.00988% | 10,119 |
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.Cys434=
- Coding
- c.1302C>T
- MANE Select
- NM_139072
- dbSNP
- rs140576705
- Type
- single nucleotide variant
- Location
- chr2:229447500 (GRCh38)
- Gene constraint
- LOEUF 0.561 · pLI 0.21 (gnomAD)
- Structure
- AlphaFold pLDDT 70.51
- Residue 434
- the egf-like 6 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-cys434 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown