Is ULK3 p.Ala31= (c.93C>T) pathogenic?

ULK3 p.Ala31= (c.93C>T) is classified Likely benign in ULK3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-01). Ultra-rare (popmax 0.0178%, amr).

How common is ULK3 p.Ala31= (c.93C>T) in the general population?

ULK3 p.Ala31= (c.93C>T) is ultra-rare (popmax 0.0178%, amr) (gnomAD).

ULK3 p.Ala31=

c.93C>T · rs774909124 · VCV2645550

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0178%, amr)

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 4.3	GERP 0.18, phastCons 1
Overall
CADD	15.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0178% Admixed American · 9/50,586 alleles

Filtering AF 0.0103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00976%

Overall 0.01% 155/1,546,776 alleles · ultra-rare exomes 140/1,394,564 · genomes 15/152,212 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0178%	5,621
European (non-Finnish)	0.012%	8,302
Remaining individualsnot grpmax-eligible	0.0117%	8,552
Finnishnot grpmax-eligible	0.00171%	58,352

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: ULK3
Protein: p.Ala31=
Coding: c.93C>T
MANE Select: NM_001099436
dbSNP: rs774909124
Type: single nucleotide variant
Location: chr15:74843013 (GRCh38)
Gene constraint: LOEUF 1.161 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.96 · 3 PDB
Residue 31: the protein kinase domain; a β-strand

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.Ala286Val Uncertain significance ★ ⚠ same type
ULK3 p.Ala303Thr 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-ala31 (accessed [today's date]).

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