Is TENT4A p.Arg792Thr (c.2375G>C) pathogenic?

TENT4A p.Arg792Thr (c.2375G>C) is classified Uncertain significance in TENT4A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-03). Absent from gnomAD v4.1.

How common is TENT4A p.Arg792Thr (c.2375G>C) in the general population?

TENT4A p.Arg792Thr (c.2375G>C) is absent from gnomAD v4.1 (gnomAD).

TENT4A p.Arg792Thr

c.2375G>C · rs1364142323 · VCV3176010

Uncertain significance Single submitter

Classification

Uncertain significance

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.
REVEL	0.252	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 5,315 bp · p 0.67 · regional, not allelic
Overall
CADD	27.0	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: TENT4A
Protein: p.Arg792Thr
Coding: c.2375G>C
MANE Select: NM_006999
dbSNP: rs1364142323
Type: single nucleotide variant
Location: chr5:6754941 (GRCh38)
Gene constraint: LOEUF 0.208 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 62.58
Residue 792: the 'disordered' region

Full TENT4A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TENT4A p.Arg792Gly Uncertain significance ★ same residue
TENT4A p.Glu307Ala Uncertain significance ★★ same type
CERT1 p.Phe19Cys Likely benign ★★ same type
POLK p.Asn753= Benign ★★ same type
POLK p.Glu762= Likely benign ★★ same type
POLK c.*66T>C Pathogenic ★ same type
POLK p.Ala428= Pathogenic ★ same type
POLK p.Asp551Val Pathogenic ★ ⚠ 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/tent4a-p-arg792thr (accessed [today's date]).

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