Is ULK4 p.His55= (c.165C>T) pathogenic?

ULK4 p.His55= (c.165C>T) is classified Likely benign in ULK4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-30). Rare (popmax 0.181%, afr); Associated with ULK4-related disorder.

What condition is associated with ULK4 p.His55= (c.165C>T)?

ULK4 p.His55= (c.165C>T) is associated with ULK4-related disorder (ClinVar).

How common is ULK4 p.His55= (c.165C>T) in the general population?

ULK4 p.His55= (c.165C>T) is rare (popmax 0.181%, afr) (gnomAD).

ULK4 p.His55=

c.165C>T · rs199939738 · VCV3056778

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.181%, afr)

Conditions

ULK4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 5	GERP -0.26, phastCons 1
Overall
CADD	9.514	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.181% African / African-American · 136/74,986 alleles

Filtering AF 0.157% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.147%

Overall 0.00955% 154/1,612,876 alleles · rare exomes 67/1,460,726 · genomes 87/152,150 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.181%	551
Admixed American	0.0183%	5,450
Remaining individualsnot grpmax-eligible	0.0112%	8,921

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: ULK4
Protein: p.His55=
Coding: c.165C>T
MANE Select: NM_017886
dbSNP: rs199939738
Type: single nucleotide variant
Location: chr3:41938171 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.59 · 2 PDB
Residue 55: the protein kinase domain

Full ULK4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ULK4-related disorder

Similar variants

ULK4 c.1764+3G>A Likely benign same condition
ULK4 c.896+5T>G Likely benign same condition
ULK4 p.Ala715Thr Benign same condition
ULK4 p.Asn796= Likely benign same condition
ULK4 p.Gln387Arg Likely benign same condition
ULK4 p.Gly352= Benign same condition
ULK4 p.Leu1084= Likely benign same condition
ULK4 p.Leu603Ser Benign 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/ulk4-p-his55 (accessed [today's date]).

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