PHOX2B p.Ala265=
c.795G>C · rs1440737466 · VCV1557763
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00313%, sas)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -3.8, phastCons 0.97 |
| Overall | ||
| CADD | 9.296 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00313%
South Asian · 2/63,948 alleles
Filtering AF
0.000519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000194%
Overall
0.000208%
3/1,445,612 alleles · very rare
exomes 2/1,295,530 · genomes 1/150,082 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00313% | 31,974 |
| European (non-Finnish) | 9.14e-05% | 1,093,526 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PHOX2B
- Protein
- p.Ala265=
- Coding
- c.795G>C
- MANE Select
- NM_003924
- dbSNP
- rs1440737466
- Type
- single nucleotide variant
- Location
- chr4:41745957 (GRCh38)
- Gene constraint
- LOEUF 0.349 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.94 · 5 PDB
- Residue 265
- a β-strand; the 'disordered' region
Similar variants
- PHOX2B p.Ala265Thr Uncertain significance ★★ ⚠ same residue
- PHOX2B p.Ala265Glu Uncertain significance ★ ⚠ same residue
- PHOX2B p.Ala265Gly Uncertain significance ★ ⚠ same residue
- PHOX2B p.Ala265Val Uncertain significance ★ ⚠ same residue
- PHOX2B c.241+1G>A Likely pathogenic ★★ same condition
- PHOX2B c.242-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PHOX2B p.Arg141Gln Pathogenic/Likely pathogenic ★★ same condition
- PHOX2B p.Gln98Ter Pathogenic ★★ 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/phox2b-p-ala265 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown