Is ARID2 p.Lys35Ter (c.103A>T) pathogenic?

ARID2 p.Lys35Ter (c.103A>T) is classified Likely pathogenic in ARID2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-05-29). No allele count reported in gnomAD v4.1 (AN 1,613,240); Associated with Coffin-Siris syndrome 6.

What condition is associated with ARID2 p.Lys35Ter (c.103A>T)?

ARID2 p.Lys35Ter (c.103A>T) is associated with Coffin-Siris syndrome 6 (ClinVar).

How common is ARID2 p.Lys35Ter (c.103A>T) in the general population?

ARID2 p.Lys35Ter (c.103A>T) is no allele count reported in gnomAD v4.1 (AN 1,613,240) (gnomAD).

ARID2 p.Lys35Ter

c.103A>T · VCV3347919

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,240)

Conditions

Coffin-Siris syndrome 6

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 6	GERP 0.55, phastCons 1
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,240). 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.Lys35Ter
Coding: c.103A>T
Type: single nucleotide variant
Location: chr12:45730054 (GRCh38)

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

Disease context

Coffin-Siris syndrome 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-lys35ter (accessed [today's date]).

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