Is LYN p.Thr37= (c.111G>A) pathogenic?

LYN p.Thr37= (c.111G>A) is classified Likely benign in LYN (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-04). Ultra-rare (popmax 0.0111%, eas).

How common is LYN p.Thr37= (c.111G>A) in the general population?

LYN p.Thr37= (c.111G>A) is ultra-rare (popmax 0.0111%, eas) (gnomAD).

LYN p.Thr37=

c.111G>A · rs56094668 · VCV2918671

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, eas)

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 8.7	GERP 1.7, phastCons 1
Overall
CADD	16.05	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0111% East Asian · 5/44,848 alleles

Filtering AF 0.00435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00276%

Overall 0.00062% 10/1,613,408 alleles · ultra-rare exomes 9/1,461,296 · genomes 1/152,112 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0111%	8,970
African / African-American	0.00267%	37,436
European (non-Finnish)	0.000254%	393,272

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: LYN
Protein: p.Thr37=
Coding: c.111G>A
MANE Select: NM_002350
dbSNP: rs56094668
Type: single nucleotide variant
Location: chr8:55941970 (GRCh38)
Gene constraint: LOEUF 0.282 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.44 · 6 PDB
Residue 37: the 'disordered' region

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

Similar variants

LYN p.Thr37Ala Uncertain significance ★ ⚠ same residue
LYN p.Thr37Met Uncertain significance ★ ⚠ same residue
LYN p.Ala150Thr Uncertain significance ★★ ⚠ same type
LYN p.Ala70Thr Uncertain significance ★★ ⚠ same type
LYN p.Arg360Trp Uncertain significance ★★ ⚠ same type
LYN p.Glu47Asp Uncertain significance ★★ ⚠ same type
LYN p.Ile227Val Uncertain significance ★★ ⚠ same type
LYN p.Ser333Asn 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/lyn-p-thr37 (accessed [today's date]).

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