What condition is associated with FYN p.Thr97Ala (c.289A>G)?

FYN p.Thr97Ala (c.289A>G) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is FYN p.Thr97Ala (c.289A>G) in the general population?

FYN p.Thr97Ala (c.289A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FYN p.Thr97Ala (c.289A>G)?

AlphaMissense predicts likely pathogenic (score 0.6527) — an in-silico prediction, not a clinical call.

FYN p.Thr97Ala

Q: Is FYN p.Thr97Ala (c.289A>G) pathogenic?

FYN p.Thr97Ala (c.289A>G) is classified Pathogenic in FYN (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely pathogenic (0.6527); Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

c.289A>G · rs370573757 · VCV2681290

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6527 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
AlphaMissense	0.6527	likely pathogenic ✓ concordant with ClinVar
REVEL	0.229	benign-leaning
SaProt	LLR -9.67	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 2.8, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 12 kb · p 3.8e-05 · regional, not allelic
Overall
CADD	24.9	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

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: FYN
Protein: p.Thr97Ala
Coding: c.289A>G
MANE Select: NM_002037
dbSNP: rs370573757
Type: single nucleotide variant
Location: chr6:111714402 (GRCh38)
Gene constraint: LOEUF 0.215 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.62 · 53 PDB
Residue 97: the sh3 domain; a β-strand

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

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

FYN p.Arg96Gly Pathogenic same condition
FYN p.Arg96Trp Pathogenic same condition
FYN p.Asp506Glu Benign ★★ same type
FYN c.344+1G>A Uncertain significance ★ same type
FYN p.Ala55Thr Uncertain significance ★ ⚠ same type
FYN p.Arg123Cys Uncertain significance ★ ⚠ same type
FYN p.Arg161Ter Uncertain significance ★ same type
FYN p.Arg29Cys Uncertain significance ★ ⚠ same type

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/fyn-p-thr97ala (accessed [today's date]).

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