Is ATL3 p.Phe438= (c.1314C>T) pathogenic?

ATL3 p.Phe438= (c.1314C>T) is classified Likely benign in ATL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-17). Absent from gnomAD v4.1; Associated with neuropathy, hereditary sensory, type 1F.

What condition is associated with ATL3 p.Phe438= (c.1314C>T)?

ATL3 p.Phe438= (c.1314C>T) is associated with neuropathy, hereditary sensory, type 1F (ClinVar).

How common is ATL3 p.Phe438= (c.1314C>T) in the general population?

ATL3 p.Phe438= (c.1314C>T) is absent from gnomAD v4.1 (gnomAD).

ATL3 p.Phe438=

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.1314C>T · rs753374637 · VCV1104442

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 looked up on this page · why
Constraint at this position
Conservation	phyloP -0.044	GERP 1.3, phastCons 0.14
Overall
CADD	10.33	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: ATL3
Protein: p.Phe438=
Coding: c.1314C>T
dbSNP: rs753374637
Type: single nucleotide variant
Location: chr11:63631265 (GRCh38)

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

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-phe438 (accessed [today's date]).

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