Is NECTIN1 p.Phe23= (c.69C>T) pathogenic?

NECTIN1 p.Phe23= (c.69C>T) is classified Likely benign in NECTIN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-21). Absent from gnomAD v4.1.

How common is NECTIN1 p.Phe23= (c.69C>T) in the general population?

NECTIN1 p.Phe23= (c.69C>T) is absent from gnomAD v4.1 (gnomAD).

NECTIN1 p.Phe23=

c.69C>T · VCV4767836

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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	GERP -0.028, phastCons 1
Overall
CADD	13.18	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NECTIN1
Protein: p.Phe23=
Coding: c.69C>T
MANE Select: NM_002855
Type: single nucleotide variant
Location: chr11:119728485 (GRCh38)
Gene constraint: LOEUF 0.659 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.80 · 6 PDB

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

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-phe23 (accessed [today's date]).

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