NECTIN1 p.Pro340=
c.1020G>A · rs766791883 · VCV3049712
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00261%, eas)
Conditions
1
NECTIN1-related disorder
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 -6.4 | GERP -3.6 |
| Overall | ||
| CADD | 3.539 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00261%
East Asian · 1/38,328 alleles
Overall
0.000133%
2/1,505,756 alleles · very rare
exomes 1/1,357,308 · genomes 1/148,448 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00261% | 38,328 |
| African / African-American | 0.00141% | 70,844 |
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
- NECTIN1
- Protein
- p.Pro340=
- Coding
- c.1020G>A
- MANE Select
- NM_002855
- dbSNP
- rs766791883
- Type
- single nucleotide variant
- Location
- chr11:119665281 (GRCh38)
- Gene constraint
- LOEUF 0.659 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.80 · 6 PDB
- Residue 340
- a UniProt-annotated variant site (in edmi); a UniProt-annotated variant site (in edmi and ofc7)
Disease context
NECTIN1-related disorder
Similar variants
- NECTIN1 p.Pro340Gln Uncertain significance ★★ ⚠ same residue
- NECTIN1 c.1003+534G>A Likely benign same condition
- NECTIN1 c.1003+557G>T Benign same condition
- NECTIN1 c.79+9G>A Likely benign same condition
- NECTIN1 p.Ala351= Likely benign same condition
- NECTIN1 p.Asp46= Likely benign same condition
- NECTIN1 p.Gln409= Likely benign same condition
- NECTIN1 p.Thr21= Likely benign same condition
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/nectin1-p-pro340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown