HNRNPUL2

protein-coding

heterogeneous nuclear ribonucleoprotein U like 2

Gene summary

Enables RNA binding activity. Predicted to be involved in alternative mRNA splicing, via spliceosome. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

HNRPUL2

MANE transcript

NM_001079559.3

Inheritance

ClinVar variants

P:4U:108B:6

Top phenotype

complex neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr11:62,712,630-62,727,457

External References & Databases

Ensembl (ENSG00000214753)

Transcript & Mutation Effects

hg38 • Region Span ~14.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HNRNPUL2 variants in ClinVar

5 Conditions Cataloged

Inborn genetic diseasesTotal: 105

HNRNPUL2-related disorderTotal: 12

not providedTotal: 6

not specifiedTotal: 2

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079559.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			105 clinvar	2 clinvar		107
nonsense	1 clinvar	2 clinvar	1 clinvar			4
start loss						0
frameshift	1 clinvar		2 clinvar			3
splice donor/acceptor (+/-2bp)						0
Total	2	2	108	6	0	118

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079559.3	RefSeq	NP_001073027.1	14	MANE Select
ENST00000301785.7	Ensembl	ENSP00000301785.5	14	MANE Select
ENST00000855865.1	Ensembl	ENSP00000525924.1	14	Standard
ENST00000855865.2	Ensembl	ENSP00000525924.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

RNA binding

Cellular Component

nucleus
nucleoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301785
Coding exons: 14
Length: 14720
Individuals with no LoFs: 124789
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 124794
p: 0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.956	355	409	0.867	0.0000235	4811
Missense (PolyPhen)		67	108.85	0.61551		1170
Synonymous	-3.07	203	154	1.31	0.00000810	1436
Loss of Function	5.62	5	46.3	0.108	0.00000293	480

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.135

Intolerance Scores

LoFtool: 0.0912
RVIS EVS: -0.38
RVIS percentile EVS: 28.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.920

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium