Is ALK p.Asp769= (c.2307C>T) pathogenic?

ALK p.Asp769= (c.2307C>T) is classified Benign/Likely benign in ALK (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-26). Ultra-rare (popmax 0.0801%, sas); Associated with neuroblastoma, susceptibility to, 3.

What condition is associated with ALK p.Asp769= (c.2307C>T)?

ALK p.Asp769= (c.2307C>T) is associated with neuroblastoma, susceptibility to, 3, hereditary neoplastic syndrome (ClinVar).

How common is ALK p.Asp769= (c.2307C>T) in the general population?

ALK p.Asp769= (c.2307C>T) is ultra-rare (popmax 0.0801%, sas) (gnomAD).

ALK p.Asp769=

c.2307C>T · rs553770508 · VCV1167915

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0801%, sas)

Conditions

neuroblastoma, susceptibility to, 3

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 3.9	GERP 1.1, phastCons 1
Overall
CADD	3.855	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0801% South Asian · 73/91,082 alleles

Filtering AF 0.0654% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0599%

Overall 0.00458% 74/1,614,074 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0801%	1,248
European (non-Finnish)	8.47e-05%	1,180,034

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.Asp769=
Coding: c.2307C>T
MANE Select: NM_004304
dbSNP: rs553770508
Type: single nucleotide variant
Location: chr2:29239728 (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

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

Also linked: hereditary neoplastic syndrome

Similar variants

ALK p.Asp769Asn Uncertain significance ★★ ⚠ same residue
ALK p.Asp769Gly Uncertain significance ★★ ⚠ same residue
ALK p.Asp769Val Uncertain significance ★★ ⚠ same residue
ALK p.Asp769Glu 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-asp769 (accessed [today's date]).

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