NDP p.Arg64=
c.192G>A · VCV4761819
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.003%, eas)
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 0.53 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 14.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.003%
East Asian · 1/33,372 alleles
Filtering AF
9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5e-05%
Overall
0.000333%
4/1,201,729 alleles · very rare
exomes 3/1,089,583 · genomes 1/112,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.003% | 33,372 |
| European (non-Finnish) | 0.000337% | 296,998 |
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
- NDP
- Protein
- p.Arg64=
- Coding
- c.192G>A
- MANE Select
- NM_000266
- Type
- single nucleotide variant
- Location
- chrX:43950009 (GRCh38)
- Structure
- AlphaFold pLDDT 83.92 · 12 PDB
- Residue 64
- the ctck domain; a β-strand
Similar variants
- NDP p.Ala118Asp Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg109Ter Pathogenic ★★ same type
- NDP p.Arg115Ter Pathogenic ★★ same type
- NDP p.Arg121Trp Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg37Ter Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg38Cys Pathogenic ★★ same type
- NDP p.Arg74Cys Pathogenic ★★ same type
- NDP p.Cys110Phe Likely pathogenic ★★ 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/ndp-p-arg64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown