Is ATL3 p.Arg533= (c.1599A>G) pathogenic?

ATL3 p.Arg533= (c.1599A>G) is classified Benign in ATL3 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-21). Common (popmax 7.31%, sas) — too common for a highly-penetrant pathogenic allele; Associated with neuropathy, hereditary sensory, type 1F.

What condition is associated with ATL3 p.Arg533= (c.1599A>G)?

ATL3 p.Arg533= (c.1599A>G) is associated with neuropathy, hereditary sensory, type 1F (ClinVar).

ATL3 p.Arg533=

Q: How common is ATL3 p.Arg533= (c.1599A>G) in the general population?

ATL3 p.Arg533= (c.1599A>G) is common (popmax 7.31%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is Hereditary sensory and autonomic neuropathy type 1 inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.1599A>G · rs201636843 · VCV474837

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 7.31%, sas) — too common for a highly-penetrant pathogenic allele

Conditions

neuropathy, hereditary sensory, type 1F

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 0.16	GERP -1.8, phastCons 0.89
Overall
CADD	2.463	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.31% South Asian · 6,657/91,068 alleles

Filtering AF 7.16% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.1%

Overall 0.445% 7,183/1,614,128 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	7.31%	14
Remaining individualsnot grpmax-eligible	0.534%	187
Middle Eastern	0.495%	202
Admixed American	0.0183%	5,456
European (non-Finnish)	0.0116%	8,613
African / African-American	0.0107%	9,380
East Asian	0.00891%	11,220
Finnishnot grpmax-eligible	0.00312%	32,022

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: ATL3
Protein: p.Arg533=
Coding: c.1599A>G
MANE Select: NM_015459
dbSNP: rs201636843
Type: single nucleotide variant
Location: chr11:63629346 (GRCh38)
Gene constraint: LOEUF 0.891 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.30 · 2 PDB

Full ATL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neuropathy, hereditary sensory, type 1F — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hereditary sensory and autonomic neuropathy type 1 (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages

Similar variants

ATL3 p.Arg533Lys Uncertain significance ★ ⚠ same residue
ATL3 c.1035+1G>A Uncertain significance ★★ same condition
ATL3 c.46+1G>A Uncertain significance ★★ same condition
ATL3 c.619-4A>G Uncertain significance ★★ same condition
ATL3 c.711+1G>T Uncertain significance ★★ same condition
ATL3 c.850+5G>A Uncertain significance ★★ same condition
ATL3 p.Ala457Val Uncertain significance ★★ ⚠ same condition
ATL3 p.Ala508Thr 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/atl3-p-arg533 (accessed [today's date]).

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