Is TAB2 p.Ser582Pro (c.1744T>C) pathogenic?

TAB2 p.Ser582Pro (c.1744T>C) is classified Uncertain significance in TAB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-22). AlphaMissense: likely pathogenic (0.6875); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with TAB2 p.Ser582Pro (c.1744T>C)?

TAB2 p.Ser582Pro (c.1744T>C) is associated with Inborn genetic diseases (ClinVar).

How common is TAB2 p.Ser582Pro (c.1744T>C) in the general population?

TAB2 p.Ser582Pro (c.1744T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TAB2 p.Ser582Pro (c.1744T>C)?

AlphaMissense predicts likely pathogenic (score 0.6875) — an in-silico prediction, not a clinical call.

TAB2 p.Ser582Pro

c.1744T>C · rs2483486877 · VCV3173210

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6875 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6875	likely pathogenic
REVEL	0.344	indeterminate
SaProt	LLR -9.23	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.6, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 20 kb · p 7.3e-06 · regional, not allelic
Overall
CADD	27.7	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: TAB2
Protein: p.Ser582Pro
Coding: c.1744T>C
MANE Select: NM_001292034
dbSNP: rs2483486877
Type: single nucleotide variant
Location: chr6:149397744 (GRCh38)
Gene constraint: LOEUF 0.117 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 53.24 · 6 PDB
Residue 582: a modified residue (phosphoserine)

Full TAB2 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

TAB2 p.Ala618Val Uncertain significance ★★ ⚠ same condition
TAB2 p.Arg72His Uncertain significance ★★ ⚠ same condition
TAB2 p.Arg96Ser Uncertain significance ★★ same condition
TAB2 p.Asn118Tyr Uncertain significance ★★ ⚠ same condition
TAB2 p.Asn669Thr Uncertain significance ★★ ⚠ same condition
TAB2 p.Gln209Lys Uncertain significance ★★ ⚠ same condition
TAB2 p.Glu49Lys Uncertain significance ★★ ⚠ same condition
TAB2 p.Glu93Lys 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/tab2-p-ser582pro (accessed [today's date]).

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