Is TNC p.Ala1798= (c.5394T>A) pathogenic?

TNC p.Ala1798= (c.5394T>A) is classified Likely benign in TNC (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-08). Absent from gnomAD v4.1; Associated with TNC-related disorder.

What condition is associated with TNC p.Ala1798= (c.5394T>A)?

TNC p.Ala1798= (c.5394T>A) is associated with TNC-related disorder (ClinVar).

How common is TNC p.Ala1798= (c.5394T>A) in the general population?

TNC p.Ala1798= (c.5394T>A) is absent from gnomAD v4.1 (gnomAD).

TNC p.Ala1798=

c.5394T>A · VCV3353110

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

TNC-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.263	benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.6	GERP -0.41, phastCons 1
Overall
CADD	11.79	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: TNC
Protein: p.Ala1798=
Coding: c.5394T>A
MANE Select: NM_002160
Type: single nucleotide variant
Location: chr9:115038379 (GRCh38)
Gene constraint: LOEUF 0.608 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.48 · 21 PDB
Residue 1798: the fibronectin type-iii 13 domain

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

Disease context

TNC-related disorder

Similar variants

TNC p.Asp520Asn Uncertain significance ★ ⚠ same condition
TNC p.Gly493Arg Conflicting classifications of pathogenicity ★ ⚠ same condition
TNC p.Ser760Gly Uncertain significance ★ ⚠ same condition
TNC p.Val902Ile Conflicting classifications of pathogenicity ★ ⚠ same condition
TNC p.Ala115Thr Uncertain significance ⚠ same condition
TNC p.Asn410Ser Uncertain significance ⚠ same condition
TNC p.Glu1297Lys Uncertain significance ⚠ same condition
TNC p.Gly203Val Conflicting classifications of pathogenicity ⚠ 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/tnc-p-ala1798 (accessed [today's date]).

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