Is SH2B3 p.Ser328= (c.984C>T) pathogenic?

SH2B3 p.Ser328= (c.984C>T) is classified Likely benign in SH2B3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-23). Very rare (popmax 0.00695%, nfe); Associated with Inborn genetic diseases.

What condition is associated with SH2B3 p.Ser328= (c.984C>T)?

SH2B3 p.Ser328= (c.984C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SH2B3 p.Ser328= (c.984C>T) in the general population?

SH2B3 p.Ser328= (c.984C>T) is very rare (popmax 0.00695%, nfe) (gnomAD).

SH2B3 p.Ser328=

c.984C>T · VCV3440774

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00695%, 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 1.3	GERP -1.7, phastCons 0.93
Overall
CADD	8.723	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00695% European (non-Finnish) · 82/1,179,826 alleles

Filtering AF 0.00571% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00525%

Overall 0.00551% 89/1,613,836 alleles · very rare exomes 87/1,461,634 · genomes 2/152,202 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00695%	14,388
Admixed American	0.00333%	30,000
South Asian	0.00329%	30,361
Remaining individualsnot grpmax-eligible	0.0032%	31,234

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.Ser328=
Coding: c.984C>T
MANE Select: NM_005475
Type: single nucleotide variant
Location: chr12:111447182 (GRCh38)
Gene constraint: LOEUF 1.35 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.45
Residue 328: a UniProt-annotated variant site (found in a patient with isolated erythrocytosis; uncertain significance); the 'disordered' region

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.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
SH2B3 p.Arg226Trp Uncertain significance ★★ ⚠ same condition
SH2B3 p.Arg235Cys Uncertain significance ★★ ⚠ same condition
SH2B3 p.Arg39Gln Uncertain significance ★★ ⚠ same condition
SH2B3 p.Asp231Tyr 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-ser328 (accessed [today's date]).

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