Is VIP p.Val85Asp (c.254T>A) pathogenic?

VIP p.Val85Asp (c.254T>A) is classified Uncertain significance in VIP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-28). AlphaMissense: likely pathogenic (0.9158); Absent from gnomAD v4.1.

How common is VIP p.Val85Asp (c.254T>A) in the general population?

VIP p.Val85Asp (c.254T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about VIP p.Val85Asp (c.254T>A)?

AlphaMissense predicts likely pathogenic (score 0.9158) — an in-silico prediction, not a clinical call.

VIP p.Val85Asp

c.254T>A · rs2517743086 · VCV3188564

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9158 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9158	likely pathogenic
REVEL	0.377	indeterminate
SaProt	LLR -12.10	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.8	GERP 2.1, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 4,960 bp · p 0.5 · regional, not allelic
Overall
CADD	26.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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: VIP
Protein: p.Val85Asp
Coding: c.254T>A
dbSNP: rs2517743086
Type: single nucleotide variant
Location: chr6:152755292 (GRCh38)

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

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/vip-p-val85asp (accessed [today's date]).

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