Is BEND5 p.Ile404Val (c.1210A>G) pathogenic?

BEND5 p.Ile404Val (c.1210A>G) is classified Uncertain significance in BEND5 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely pathogenic (0.9596); Absent from gnomAD v4.1; Associated with prostate cancer.

What condition is associated with BEND5 p.Ile404Val (c.1210A>G)?

BEND5 p.Ile404Val (c.1210A>G) is associated with prostate cancer (ClinVar).

How common is BEND5 p.Ile404Val (c.1210A>G) in the general population?

BEND5 p.Ile404Val (c.1210A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BEND5 p.Ile404Val (c.1210A>G)?

AlphaMissense predicts likely pathogenic (score 0.9596) — an in-silico prediction, not a clinical call.

BEND5 p.Ile404Val

c.1210A>G · rs193921115 · VCV161769

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9596 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

prostate cancer

Computational evidence

Protein change
AlphaMissense	0.9596	likely pathogenic
REVEL	0.251	benign-leaning
SaProt	LLR -6.81	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.9	GERP 2.8, phastCons 1
Regional constraint	o/e 0.50	unconstrained · MANE · 15 kb · p 1.6e-09 · regional, not allelic
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: BEND5
Protein: p.Ile404Val
Coding: c.1210A>G
MANE Select: NM_032785 · reported on NM_024603
dbSNP: rs193921115
Type: single nucleotide variant
Location: chr1:48727942 (GRCh38)

Full BEND5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

prostate cancer — 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/bend5-p-ile404val (accessed [today's date]).

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