Is NECTIN1 p.Arg94= (c.282C>T) pathogenic?

NECTIN1 p.Arg94= (c.282C>T) is classified Likely benign in NECTIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-03). Ultra-rare (popmax 0.0107%, afr).

How common is NECTIN1 p.Arg94= (c.282C>T) in the general population?

NECTIN1 p.Arg94= (c.282C>T) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

NECTIN1 p.Arg94=

c.282C>T · rs150290487 · VCV2711598

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, 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 -4.8	GERP -3.6
Overall
CADD	0.492	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/75,036 alleles

Filtering AF 0.00791% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00744%

Overall 0.00793% 128/1,614,182 alleles · ultra-rare exomes 108/1,461,878 · genomes 20/152,304 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,380
Admixed American	0.01%	10,005
European (non-Finnish)	0.00941%	10,631
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
Remaining individualsnot grpmax-eligible	0.0032%	31,255

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.Arg94=
Coding: c.282C>T
MANE Select: NM_002855
dbSNP: rs150290487
Type: single nucleotide variant
Location: chr11:119678563 (GRCh38)
Gene constraint: LOEUF 0.659 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.80 · 6 PDB
Residue 94: the ig-like v-type domain; a turn

Full NECTIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NECTIN1 p.Arg94His Uncertain significance ★ ⚠ same residue
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

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-arg94 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown