Is ARID5A p.Pro508= (c.1524G>A) pathogenic?

ARID5A p.Pro508= (c.1524G>A) is classified Likely benign in ARID5A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-06-05). Low-frequency (popmax 1.57%, afr); Associated with ARID5A-related disorder.

What condition is associated with ARID5A p.Pro508= (c.1524G>A)?

ARID5A p.Pro508= (c.1524G>A) is associated with ARID5A-related disorder (ClinVar).

How common is ARID5A p.Pro508= (c.1524G>A) in the general population?

ARID5A p.Pro508= (c.1524G>A) is low-frequency (popmax 1.57%, afr) (gnomAD).

ARID5A p.Pro508=

c.1524G>A · rs36068522 · VCV3055644

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.57%, afr)

Conditions

ARID5A-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 -6.5	GERP -3.5
Overall
CADD	0.124	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.57% African / African-American · 1,159/74,006 alleles

Filtering AF 1.49% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.46%

Overall 0.0852% 1,339/1,570,938 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.57%	64
Admixed American	0.121%	826
Remaining individualsnot grpmax-eligible	0.0892%	1,122
Middle Eastern	0.0512%	1,952
South Asian	0.00476%	20,988
European (non-Finnish)	0.00449%	22,271

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: ARID5A
Protein: p.Pro508=
Coding: c.1524G>A
MANE Select: NM_212481
dbSNP: rs36068522
Type: single nucleotide variant
Location: chr2:96552052 (GRCh38)
Gene constraint: LOEUF 0.802 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.26

Full ARID5A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ARID5A-related disorder

Similar variants

ARID5A p.Pro432Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
ARID5A p.Pro532Leu Uncertain significance ★ ⚠ same condition
ARID5A c.571-4C>A Likely benign same condition
ARID5A p.Gly194Glu Likely benign same condition
ARID5A p.Leu304Pro Likely benign same condition
ARID5A p.Val484= Likely benign same condition
ARID5A p.Ala127Val Uncertain significance ★ ⚠ same type
ARID5A p.Ala182Thr 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/arid5a-p-pro508 (accessed [today's date]).

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