Is ALK p.Ala1459Ser (c.4375G>T) pathogenic?

ALK p.Ala1459Ser (c.4375G>T) is classified Conflicting classifications of pathogenicity in ALK (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.0764); Ultra-rare (popmax 0.0708%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with ALK p.Ala1459Ser (c.4375G>T)?

ALK p.Ala1459Ser (c.4375G>T) is associated with hereditary neoplastic syndrome, neuroblastoma, susceptibility to, 3 (ClinVar).

How common is ALK p.Ala1459Ser (c.4375G>T) in the general population?

ALK p.Ala1459Ser (c.4375G>T) is ultra-rare (popmax 0.0708%, afr) (gnomAD).

What do computational predictors say about ALK p.Ala1459Ser (c.4375G>T)?

AlphaMissense predicts likely benign (score 0.0764) — an in-silico prediction, not a clinical call.

ALK p.Ala1459Ser

c.4375G>T · rs372612147 · VCV335689

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0764 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0708%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.0764	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -6.12	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.34	GERP -2, phastCons 0.02
Regional constraint	o/e 1.10	unconstrained · MANE · 4,393 bp · p 0.054 · regional, not allelic
Overall
CADD	4.598	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 0.0708% African / African-American · 53/74,808 alleles

Filtering AF 0.0556% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0502%

Overall 0.00379% 61/1,608,938 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0708%	1,411
Middle Eastern	0.0166%	6,038
Admixed American	0.00503%	19,882
Remaining individualsnot grpmax-eligible	0.00482%	20,749
European (non-Finnish)	8.5e-05%	1,176,418

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.Ala1459Ser
Coding: c.4375G>T
MANE Select: NM_004304
dbSNP: rs372612147
Type: single nucleotide variant
Location: chr2:29193712 (GRCh38)
Gene constraint: LOEUF 0.562 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.26 · 79 PDB
Residue 1459: the 'disordered' region

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: neuroblastoma, susceptibility to, 3

Similar variants

ALK p.Ala1459Val Uncertain significance ★★ ⚠ same residue
ALK p.Ala1459Thr Uncertain significance ★ ⚠ same residue
ALK p.Ala1459= Likely benign ★ same residue
ALK p.Ala1459_Ile1461delinsValGluVal Uncertain significance ★ 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

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-ala1459ser (accessed [today's date]).

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