ARAP1 p.Trp841Ter
c.2522G>A · rs2496945980 · VCV2579707
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
autism
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 18 of 35 |
| Splicing | ||
| SpliceAI | Δ0.61 | donor gain · deltas |
| Pangolin | Δ0.22 | gain · loss 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 51.0 | 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
- ARAP1
- Protein
- p.Trp841Ter
- Coding
- c.2522G>A
- MANE Select
- NM_001040118
- dbSNP
- rs2496945980
- Type
- single nucleotide variant
- Location
- chr11:72699024 (GRCh38)
- Gene constraint
- LOEUF 0.572 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.81 · 1 PDB
- Residue 841
- the ph 3 domain
Similar variants
- ARAP1 p.Gln1047Glu Benign ★★ same type
- ARAP1 p.Pro1039= Benign ★★ same type
- ARAP1 p.Pro254Leu Benign ★★ same type
- ARAP1 p.Val1408Met Benign ★★ same type
- ARAP1 p.Ala1046Ser Uncertain significance ★ ⚠ same type
- ARAP1 p.Ala1124Thr Uncertain significance ★ ⚠ same type
- ARAP1 p.Ala1199Thr Uncertain significance ★ ⚠ same type
- ARAP1 p.Ala1389Thr 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/arap1-p-trp841ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown