Is ARID5B p.Pro604= (c.1812G>A) pathogenic?

ARID5B p.Pro604= (c.1812G>A) is classified Benign in ARID5B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-01). Common (popmax 6.42%, eas) — too common for a highly-penetrant pathogenic allele; Associated with ARID5B-related disorder.

What condition is associated with ARID5B p.Pro604= (c.1812G>A)?

ARID5B p.Pro604= (c.1812G>A) is associated with ARID5B-related disorder (ClinVar).

ARID5B p.Pro604=

Q: How common is ARID5B p.Pro604= (c.1812G>A) in the general population?

ARID5B p.Pro604= (c.1812G>A) is common (popmax 6.42%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1812G>A · rs117297247 · VCV3037676

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 6.42%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

ARID5B-related disorder

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 -6.3	GERP -3.5
Overall
CADD	0.445	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.42% East Asian · 2,880/44,884 alleles

Filtering AF 6.22% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.14%

Overall 0.444% 7,162/1,614,140 alleles · common exomes 6,160/1,461,864 · genomes 1,002/152,276 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	6.42%	16
Admixed American	5.34%	19
Remaining individualsnot grpmax-eligible	0.504%	198
South Asian	0.22%	455
Finnishnot grpmax-eligible	0.153%	653
African / African-American	0.0906%	1,104
Middle Eastern	0.0825%	1,212
Ashkenazi Jewishnot grpmax-eligible	0.0743%	1,346
European (non-Finnish)	0.0315%	3,172

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: ARID5B
Protein: p.Pro604=
Coding: c.1812G>A
MANE Select: NM_032199
dbSNP: rs117297247
Type: single nucleotide variant
Location: chr10:62091275 (GRCh38)
Gene constraint: LOEUF 0.211 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 51.00 · 2 PDB
Residue 604: the 'disordered' region

Full ARID5B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ARID5B-related disorder

Similar variants

ARID5B p.Pro604Leu Uncertain significance ★ ⚠ same residue
ARID5B p.Cys46Tyr Uncertain significance ★ ⚠ same condition
ARID5B p.Arg335Thr Uncertain significance ⚠ same condition
ARID5B p.Leu1095His Uncertain significance ⚠ same condition
ARID5B p.Thr441Asn Uncertain significance ⚠ same condition
ARID5B p.Ala1028= Likely benign same condition
ARID5B p.Ala533= Likely benign same condition
ARID5B p.Ala618Thr Benign 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/arid5b-p-pro604 (accessed [today's date]).

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