UBAP2L

protein-coding

ubiquitin associated protein 2 like, the group of Small nucleolar RNA protein coding host genes

Gene summary

Enables RNA binding activity. Involved in binding activity of sperm to zona pellucida; positive regulation of stress granule assembly; and stress granule assembly. Acts upstream of or within hematopoietic stem cell homeostasis. Part of PcG protein complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014847.4

Inheritance

ClinVar variants

P:16U:147B:16

Top phenotype

Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr1:154,220,179-154,271,510

External References & Databases

Ensembl (ENSG00000143569)

Transcript & Mutation Effects

hg38 • Region Span ~51.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic faciesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0957588

Submitter: PanelApp Australia

neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic faciesDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0957588

Submitter: Ambry Genetics

neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic faciesMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0957588

Submitter: G2P

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic faciesAD

Manifestation: Craniofacial; Musculoskeletal; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 35977029

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UBAP2L variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 71

Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic faciesTotal: 20

Neurodevelopmental disorderTotal: 2

UBAP2L-related conditionTotal: 2

UBAP2L-related disorderTotal: 1

Global developmental delayTotal: 1

Neurodevelopmental abnormalityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014847.4. 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		1 clinvar	5 clinvar	6 clinvar	2 clinvar	14
missense			131 clinvar	7 clinvar	1 clinvar	139
nonsense	3 clinvar	4 clinvar				7
start loss			1 clinvar			1
frameshift	3 clinvar	4 clinvar				7
splice donor/acceptor (+/-2bp)	1 clinvar		10 clinvar			11
Total	7	9	147	13	3	179

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 163 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014847.4	RefSeq	NP_055662.3	26	MANE Select
ENST00000428931.6	Ensembl	ENSP00000389445.1	26	MANE Select
NM_001127320.3	RefSeq	NP_001120792.1	24	Standard
NM_001287815.1	RefSeq	NP_001274744.1	24	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

binding of sperm to zona pellucida
hematopoietic stem cell homeostasis

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
Ada2/Gcn5/Ada3 transcription activator complex
cytoplasm
PcG protein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000428931
Coding exons: 26
Length: 51332
Individuals with no LoFs: 105021
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 105023
p: 0.00000952

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.34	382	615	0.621	0.0000342	7012
Missense (PolyPhen)		37	84.565	0.43753		907
Synonymous	-0.109	255	253	1.01	0.0000153	2259
Loss of Function	7.02	2	61.4	0.0326	0.00000324	655

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000053	0.000053	rare
European (Non-Finnish)	0.000011	0.000011	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays an important role in the activity of long-term repopulating hematopoietic stem cells (LT-HSCs). {ECO:0000250|UniProtKB:Q80X50}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.0236
RVIS EVS: -1.11
RVIS percentile EVS: 6.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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