NDP p.Arg121=
c.363G>T · rs1232013505 · VCV1529811
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00181%, nfe)
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 2.1 | GERP 0.96, phastCons 1 |
| Overall | ||
| CADD | 18.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00181%
European (non-Finnish) · 16/882,651 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000868%
Overall
0.00135%
16/1,185,066 alleles · very rare
exomes 15/1,073,275 · genomes 1/111,791 · joint denominator
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.Arg121=
- Coding
- c.363G>T
- MANE Select
- NM_000266
- dbSNP
- rs1232013505
- Type
- single nucleotide variant
- Location
- chrX:43949838 (GRCh38)
- Structure
- AlphaFold pLDDT 83.92 · 12 PDB
- Residue 121
- the ctck domain; a UniProt-annotated variant site (in nd); a UniProt-annotated variant site (in evr2); a UniProt-annotated variant site (in evr2 and nd; reduced amount of protein in the extracellular matrix); a UniProt-annotated variant site (in nd and evr2); a β-strand
Similar variants
- NDP p.Arg121Trp Pathogenic/Likely pathogenic ★★ same residue
- NDP p.Arg121Gln Pathogenic ★ ⚠ same residue
- NDP p.Arg121Leu Pathogenic ⚠ same residue
- NDP p.Ala118Asp Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg109Ter Pathogenic ★★ same type
- NDP p.Arg115Ter Pathogenic ★★ same type
- NDP p.Arg37Ter Pathogenic/Likely pathogenic ★★ same type
- NDP p.Arg38Cys 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-arg121 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown