AVPR2 c.910+6T>C
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.108 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| Splice region | donor +6 | donor splice region (+6, within the first 6 intronic nt) · inside the BP7-excluded zone |
| SpliceAI | Δ0.53 | donor loss · deltas |
| Pangolin | Δ0.24 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.38 | GERP 0.68, phastCons 0.86 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 12.72 | PHRED · no single calibrated threshold — expert panels disagree |
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
- AVPR2
- Coding
- c.910+6T>C
- MANE Select
- NM_000054
- Type
- single nucleotide variant
- Location
- chrX:153906422 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
Similar variants
- AVPR2 p.Arg104Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AVPR2 p.Arg113Trp Pathogenic ★★ same type
- AVPR2 p.Arg137Cys Pathogenic ★★ same type
- AVPR2 p.Arg137His Pathogenic ★★ same type
- AVPR2 p.Arg181Cys Pathogenic ★★ ⚠ same type
- AVPR2 p.Arg202Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AVPR2 p.Arg337Ter Pathogenic ★★ same type
- AVPR2 p.Asp85Asn 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/avpr2-c-910-plus-6t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown