Is AGT c.862C>T pathogenic?

AGT c.862C>T is classified Uncertain significance in AGT (ClinVar, Multiple submitters, 4 submitters; last evaluated 2022-11-19). AlphaMissense: likely benign (0.1025); Very rare (popmax 0.00636%, nfe); Associated with essential hypertension, genetic.

What condition is associated with AGT c.862C>T?

AGT c.862C>T is associated with essential hypertension, genetic, renal tubular dysgenesis of genetic origin (ClinVar).

How common is AGT c.862C>T in the general population?

AGT c.862C>T is very rare (popmax 0.00636%, nfe) (gnomAD).

What do computational predictors say about AGT c.862C>T?

AlphaMissense predicts likely benign (score 0.1025) — an in-silico prediction, not a clinical call.

AGT c.862C>T

rs61762530 · VCV806381

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.1025 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00636%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

essential hypertension, genetic

Computational evidence

Protein change
AlphaMissense	0.1025	likely benign
REVEL	0.177	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP 0.39, phastCons 0.42
Non-coding constraint	Z 0.14	1 kb window · o/e 0.99 · regional · uncalibrated
Overall
CADD	18.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00636% European (non-Finnish) · 75/1,179,806 alleles

Filtering AF 0.00519% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00474%

Overall 0.00775% 125/1,613,732 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.152%	658
Remaining individualsnot grpmax-eligible	0.008%	12,496
European (non-Finnish)grpmax	0.00636%	15,731

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: AGT
Coding: c.862C>T
MANE Select: NM_001384479
dbSNP: rs61762530
Type: single nucleotide variant
Location: chr1:230706168 (GRCh38)
Gene constraint: LOEUF 1.202 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.74 · 22 PDB

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

Disease context

essential hypertension, genetic — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: renal tubular dysgenesis of genetic origin

Similar variants

AGT c.1060C>T Pathogenic/Likely pathogenic ★★ same condition
AGT c.829+1G>T Pathogenic/Likely pathogenic ★★ same condition
AGT c.1195G>A Uncertain significance ★★ ⚠ same condition
AGT c.856G>T Uncertain significance ★★ ⚠ same condition
AGT c.-17G>C Uncertain significance ★★ ⚠ same condition
AGT p.Arg165Gln Uncertain significance ★★ same condition
AGT p.Arg366Leu Uncertain significance ★★ ⚠ same condition
AGT p.Arg366Trp Uncertain significance ★★ ⚠ 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/agt-c-862c-t (accessed [today's date]).

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