Is ARID2 p.Ser1713fs (c.5132_5135dup) pathogenic?

ARID2 p.Ser1713fs (c.51325135dup) is classified Pathogenic in ARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-11-20). Absent from gnomAD.

How common is ARID2 p.Ser1713fs (c.5132_5135dup) in the general population?

ARID2 p.Ser1713fs (c.5132_5135dup) is absent from gnomAD (gnomAD).

ARID2 p.Ser1713fs

c.5132_5135dup · rs2138233303 · VCV1198066

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 18 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ARID2
Protein: p.Ser1713fs
Coding: c.5132_5135dup
MANE Select: NM_152641
dbSNP: rs2138233303
Type: Duplication
Location: chr12:45892080 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 52.30 · 2 PDB
Residue 1713: the 'disordered' region; a UniProt-annotated variant site (in css6)

Full ARID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARID2 p.Gln134fs Pathogenic/Likely pathogenic ★★ same type
ARID2 p.Ile37fs Likely pathogenic ★★ same type
ARID2 p.Ala1219fs Pathogenic ★ same type
ARID2 p.Asn302fs Pathogenic ★ same type
ARID2 p.Asp1368fs Pathogenic ★ same type
ARID2 p.Asp280fs Pathogenic ★ same type
ARID2 p.Gln1404fs Pathogenic ★ same type
ARID2 p.Ile1401fs Pathogenic ★ 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/arid2-p-ser1713fs (accessed [today's date]).

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