NECTIN1 p.Ala155=
c.465A>T · rs34643468 · VCV726796
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.241%, 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 -5.5 | GERP -3.9 |
| Overall | ||
| CADD | 1.433 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.241%
African / African-American · 181/75,032 alleles
Filtering AF
0.212%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.201%
Overall
0.0122%
197/1,614,176 alleles · rare
exomes 101/1,461,886 · genomes 96/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.241% | 415 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.01% | 10,005 |
| European (non-Finnish) | 0.000169% | 590,012 |
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.Ala155=
- Coding
- c.465A>T
- MANE Select
- NM_002855
- dbSNP
- rs34643468
- Type
- single nucleotide variant
- Location
- chr11:119677823 (GRCh38)
- Gene constraint
- LOEUF 0.659 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.80 · 6 PDB
- Residue 155
- a UniProt-annotated variant site (in edmi); the ig-like c2-type 1 domain
Similar variants
- NECTIN1 c.*1139G>A Uncertain significance ★★ same type
- NECTIN1 c.*1179C>G Uncertain significance ★★ same type
- NECTIN1 c.*1595C>A Uncertain significance ★★ same type
- NECTIN1 c.*185T>C Uncertain significance ★★ same type
- NECTIN1 c.*2416A>G Uncertain significance ★★ same type
- NECTIN1 c.*3440G>A Uncertain significance ★★ same type
- NECTIN1 c.*3705G>A Uncertain significance ★★ same type
- NECTIN1 c.*607C>A 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/nectin1-p-ala155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown