Is SH2B3 p.Arg39= (c.117G>A) pathogenic?

SH2B3 p.Arg39= (c.117G>A) is classified Likely benign in SH2B3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-18). Very rare (popmax 0.000872%, nfe); Associated with Inborn genetic diseases.

What condition is associated with SH2B3 p.Arg39= (c.117G>A)?

SH2B3 p.Arg39= (c.117G>A) is associated with Inborn genetic diseases (ClinVar).

How common is SH2B3 p.Arg39= (c.117G>A) in the general population?

SH2B3 p.Arg39= (c.117G>A) is very rare (popmax 0.000872%, nfe) (gnomAD).

SH2B3 p.Arg39=

c.117G>A · VCV3953462

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000872%, nfe)

Conditions

Inborn genetic diseases

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 0.19	GERP -1.3, phastCons 0.95
Overall
CADD	6.255	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000872% European (non-Finnish) · 10/1,146,392 alleles

Filtering AF 0.000441% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000322%

Overall 0.000724% 10/1,381,406 alleles · very rare

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: SH2B3
Protein: p.Arg39=
Coding: c.117G>A
MANE Select: NM_005475
Type: single nucleotide variant
Location: chr12:111418262 (GRCh38)
Gene constraint: LOEUF 1.35 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.45

Full SH2B3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SH2B3 p.Arg39Gln Uncertain significance ★★ ⚠ same residue
SH2B3 p.Arg39Gly Uncertain significance ★ ⚠ same residue
SH2B3 p.Arg39Leu Uncertain significance ★ ⚠ same residue
SH2B3 p.Arg39Trp Uncertain significance ★ ⚠ same residue
SH2B3 p.Ala161Val Uncertain significance ★★ ⚠ same condition
SH2B3 p.Ala174Thr Uncertain significance ★★ ⚠ same condition
SH2B3 p.Ala300Thr Uncertain significance ★★ ⚠ same condition
SH2B3 p.Arg221Met 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/sh2b3-p-arg39 (accessed [today's date]).

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