Is ULK3 p.Ala286Val (c.857C>T) pathogenic?

ULK3 p.Ala286Val (c.857C>T) is classified Uncertain significance in ULK3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-13). AlphaMissense: likely benign (0.0941); No allele count reported in gnomAD v4.1 (AN 1,559,614).

How common is ULK3 p.Ala286Val (c.857C>T) in the general population?

ULK3 p.Ala286Val (c.857C>T) is no allele count reported in gnomAD v4.1 (AN 1,559,614) (gnomAD).

What do computational predictors say about ULK3 p.Ala286Val (c.857C>T)?

AlphaMissense predicts likely benign (score 0.0941) — an in-silico prediction, not a clinical call.

ULK3 p.Ala286Val

c.857C>T · rs1254719633 · VCV2244726

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0941 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,559,614)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0941	likely benign
REVEL	0.112	moderately benign-leaning
SaProt	LLR -8.63	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 8.4	GERP 0.88, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 5,874 bp · p 0.0054 · regional, not allelic
Overall
CADD	20.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

No allele count reported in gnomAD v4.1 (AN 1,559,614). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ULK3
Protein: p.Ala286Val
Coding: c.857C>T
MANE Select: NM_001099436
dbSNP: rs1254719633
Type: single nucleotide variant
Location: chr15:74839369 (GRCh38)
Gene constraint: LOEUF 1.161 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.96 · 3 PDB
Residue 286: the mit 1 domain

Full ULK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ULK3 p.Arg101His Benign ★★ same type
ULK3 p.Pro177= Benign ★★ same type
ULK3 p.Ser468= Benign ★★ same type
ULK3 p.Ala114Val Uncertain significance ★ ⚠ same type
ULK3 p.Ala192Thr Uncertain significance ★ ⚠ same type
ULK3 p.Ala26Thr Uncertain significance ★ ⚠ same type
ULK3 p.Ala303Thr Uncertain significance ★ ⚠ same type
ULK3 p.Ala378Thr 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/ulk3-p-ala286val (accessed [today's date]).

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