Is STRADA p.Arg362Cys (c.1084C>T) pathogenic?

STRADA p.Arg362Cys (c.1084C>T) is classified Uncertain significance in STRADA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-20). AlphaMissense: ambiguous (0.4183); Very rare (popmax 0.0011%, nfe); Associated with Inborn genetic diseases.

What condition is associated with STRADA p.Arg362Cys (c.1084C>T)?

STRADA p.Arg362Cys (c.1084C>T) is associated with Inborn genetic diseases (ClinVar).

How common is STRADA p.Arg362Cys (c.1084C>T) in the general population?

STRADA p.Arg362Cys (c.1084C>T) is very rare (popmax 0.0011%, nfe) (gnomAD).

What do computational predictors say about STRADA p.Arg362Cys (c.1084C>T)?

AlphaMissense predicts ambiguous (score 0.4183) — an in-silico prediction, not a clinical call.

STRADA p.Arg362Cys

c.1084C>T · VCV3802634

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4183 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4183	ambiguous
REVEL	0.487	indeterminate
SaProt	LLR -11.27	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 1.8, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 25 kb · p 5.3e-06 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% European (non-Finnish) · 13/1,179,604 alleles

Filtering AF 0.000615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.00116% 17/1,460,372 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0032%	31,221
Finnishnot grpmax-eligible	0.00157%	63,696
European (non-Finnish)grpmax	0.0011%	90,739
South Asian	0.0011%	90,856

Remaining individuals 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: STRADA
Protein: p.Arg362Cys
Coding: c.1084C>T
MANE Select: NM_001003787
Type: single nucleotide variant
Location: chr17:63704357 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.46 · 4 PDB
Residue 362: the protein kinase domain

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

Disease context

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

Similar variants

STRADA p.Arg362His Uncertain significance ★ ⚠ same residue
STRADA p.Arg100Gln Uncertain significance ★★ ⚠ same condition
STRADA p.Arg13Leu Uncertain significance ★★ ⚠ same condition
STRADA p.Asp232Gly Uncertain significance ★★ ⚠ same condition
STRADA p.Asp428Asn Uncertain significance ★★ ⚠ same condition
STRADA p.Glu422Lys Uncertain significance ★★ ⚠ same condition
STRADA p.Glu70Lys Uncertain significance ★★ ⚠ same condition
STRADA p.Gly207Arg 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/strada-p-arg362cys (accessed [today's date]).

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