Is ALK p.Gly89= (c.267C>A) pathogenic?

ALK p.Gly89= (c.267C>A) is classified Benign/Likely benign in ALK (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-04-01). Low-frequency (popmax 1.82%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with ALK p.Gly89= (c.267C>A)?

ALK p.Gly89= (c.267C>A) is associated with hereditary neoplastic syndrome, neuroblastoma, susceptibility to, 3 (ClinVar).

How common is ALK p.Gly89= (c.267C>A) in the general population?

ALK p.Gly89= (c.267C>A) is low-frequency (popmax 1.82%, afr) (gnomAD).

ALK p.Gly89=

c.267C>A · rs192127241 · VCV239812

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.82%, afr)

Conditions

hereditary neoplastic syndrome

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 1.7	GERP -2.4, phastCons 1
Overall
CADD	3.654	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.82% African / African-American · 1,348/73,982 alleles

Filtering AF 1.74% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.71%

Overall 0.0966% 1,517/1,570,148 alleles · low-frequency exomes 757/1,417,800 · genomes 760/152,348 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.82%	55
Admixed American	0.157%	638
Remaining individualsnot grpmax-eligible	0.0952%	1,050
Middle Eastern	0.0666%	1,500
European (non-Finnish)	0.0019%	52,661
South Asian	0.00117%	85,776

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.Gly89=
Coding: c.267C>A
MANE Select: NM_004304
dbSNP: rs192127241
Type: single nucleotide variant
Location: chr2:29920393 (GRCh38)
Gene constraint: LOEUF 0.562 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.26 · 79 PDB

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.Gly89Ala Uncertain significance ★★ ⚠ same residue
ALK p.Gly89Val Uncertain significance ★★ ⚠ same residue
ALK p.Gly89Ser 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-gly89 (accessed [today's date]).

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