ARID2 p.Trp264Ter
c.791G>A · rs2138126544 · VCV1705351
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Coffin-Siris syndrome 6
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 21 |
| Splicing | ||
| SpliceAI | Δ0.43 | acceptor loss, 18 bp away · masked 0 · deltas |
| Pangolin | Δ0.41 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 38.0 | 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
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
- ARID2
- Protein
- p.Trp264Ter
- Coding
- c.791G>A
- MANE Select
- NM_152641
- dbSNP
- rs2138126544
- Type
- single nucleotide variant
- Location
- chr12:45836759 (GRCh38)
- Gene constraint
- LOEUF 0.224 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.30 · 2 PDB
Similar variants
- ARID2 p.Arg1272Ter Pathogenic ★★ same condition
- ARID2 p.Arg1754Ter Pathogenic ★★ same condition
- ARID2 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same condition
- ARID2 p.Gln920Ter Pathogenic ★★ same condition
- ARID2 p.Asn302Ser Uncertain significance ★★ ⚠ same condition
- ARID2 p.Glu112Ala Uncertain significance ★★ ⚠ same condition
- ARID2 p.Glu1413Gly Uncertain significance ★★ ⚠ same condition
- ARID2 p.Ala1434Ser 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/arid2-p-trp264ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown