NCDN p.Pro664=
c.1992G>A · rs144764842 · VCV2638655
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.266%, 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 -14 | GERP -3.7 |
| Overall | ||
| CADD | 0.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.266%
South Asian · 240/90,384 alleles
Filtering AF
0.238%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.227%
Overall
0.0198%
318/1,605,954 alleles · rare
exomes 287/1,453,648 · genomes 31/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.266% | 377 |
| Middle Eastern | 0.0664% | 1,506 |
| Remaining individualsnot grpmax-eligible | 0.0225% | 4,439 |
| East Asian | 0.0224% | 4,457 |
| African / African-American | 0.00534% | 18,730 |
| European (non-Finnish) | 0.00374% | 26,741 |
| Admixed American | 0.00342% | 29,252 |
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
- NCDN
- Protein
- p.Pro664=
- Coding
- c.1992G>A
- MANE Select
- NM_014284
- dbSNP
- rs144764842
- Type
- single nucleotide variant
- Location
- chr1:35565465 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.12
Similar variants
- NCDN p.Arg259Trp Uncertain significance ★★ ⚠ same type
- NCDN p.Arg423His Uncertain significance ★★ ⚠ same type
- NCDN p.Gly164Ser Uncertain significance ★★ ⚠ same type
- NCDN p.Gly189Ser Uncertain significance ★★ ⚠ same type
- NCDN p.Arg478Gln Pathogenic ★ ⚠ same type
- NCDN p.Glu433Gln Likely pathogenic ★ ⚠ same type
- NCDN p.Pro533Leu Likely pathogenic ★ same type
- NCDN p.Pro652Leu 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/ncdn-p-pro664 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown