Is ARID3B p.Pro147Ser (c.439C>T) pathogenic?

ARID3B p.Pro147Ser (c.439C>T) is classified Uncertain significance in ARID3B (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-17). AlphaMissense: likely benign (0.067); Absent from gnomAD v4.1.

How common is ARID3B p.Pro147Ser (c.439C>T) in the general population?

ARID3B p.Pro147Ser (c.439C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARID3B p.Pro147Ser (c.439C>T)?

AlphaMissense predicts likely benign (score 0.067) — an in-silico prediction, not a clinical call.

ARID3B p.Pro147Ser

c.439C>T · rs779215718 · VCV2251531

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.067 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.067	likely benign
REVEL	0.067	moderately benign-leaning
SaProt	LLR -6.28	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.16
Regional constraint	o/e 0.74	unconstrained · MANE · 29 kb · p 6.4e-05 · regional, not allelic
Overall
CADD	10.15	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: ARID3B
Protein: p.Pro147Ser
Coding: c.439C>T
MANE Select: NM_006465
dbSNP: rs779215718
Type: single nucleotide variant
Location: chr15:74544375 (GRCh38)
Gene constraint: LOEUF 0.332 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 59.11
Residue 147: the 'disordered' region

Full ARID3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARID3B p.Arg238= Benign ★★ same type
ARID3B p.Ala164Thr Uncertain significance ★ ⚠ same type
ARID3B p.Ala342Val Uncertain significance ★ ⚠ same type
ARID3B p.Ala348Thr Uncertain significance ★ ⚠ same type
ARID3B p.Ala410Gly Uncertain significance ★ ⚠ same type
ARID3B p.Ala419Thr Uncertain significance ★ ⚠ same type
ARID3B p.Ala531Thr Uncertain significance ★ ⚠ same type
ARID3B p.Ala552Thr 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/arid3b-p-pro147ser (accessed [today's date]).

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