Is ALK p.Pro1398= (c.4194G>T) pathogenic?

ALK p.Pro1398= (c.4194G>T) is classified Likely benign in ALK (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-18). Very rare (popmax 0.0022%, sas); Associated with neuroblastoma, susceptibility to, 3.

What condition is associated with ALK p.Pro1398= (c.4194G>T)?

ALK p.Pro1398= (c.4194G>T) is associated with neuroblastoma, susceptibility to, 3 (ClinVar).

How common is ALK p.Pro1398= (c.4194G>T) in the general population?

ALK p.Pro1398= (c.4194G>T) is very rare (popmax 0.0022%, sas) (gnomAD).

ALK p.Pro1398=

c.4194G>T · rs201653228 · VCV1560485

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

neuroblastoma, susceptibility to, 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.31	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -3.2	GERP -4.7
Overall
CADD	3.563	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,068 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000137% 2/1,461,832 alleles · very rare

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: ALK
Protein: p.Pro1398=
Coding: c.4194G>T
MANE Select: NM_004304
dbSNP: rs201653228
Type: single nucleotide variant
Location: chr2:29193893 (GRCh38)
Gene constraint: LOEUF 0.562 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.26 · 79 PDB
Residue 1398: an α-helix

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

Disease context

neuroblastoma, susceptibility to, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ALK p.Pro1398Arg Uncertain significance ★★ ⚠ same residue
ALK p.Pro1398Thr Uncertain significance ★★ ⚠ same residue
ALK p.Pro1398Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
ALK p.Arg1275Gln Pathogenic ★★ same condition
ALK c.1154+5G>A Uncertain significance ★★ same condition
ALK c.1155-3C>T Uncertain significance ★★ same condition
ALK c.1282+3A>G Uncertain significance ★★ same condition
ALK c.1414+1G>A 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/alk-p-pro1398 (accessed [today's date]).

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