UBAP2L

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

Basic information

Region (hg38): 1:154220178-154271510

Links

ENSG00000143569 ∙ NCBI:9898 ∙ OMIM:616472 ∙ HGNC:29877 ∙ Uniprot:Q14157 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies	AD	General	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	Craniofacial; Musculoskeletal; Neurologic	35977029

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBAP2L gene.

• Inborn genetic diseases (21 variants)
• not provided (11 variants)
• Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBAP2L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			25			25
nonsense	1					1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region	1					1
non coding					1	1
Total	1	0	26	2	2

Variants in UBAP2L

This is a list of pathogenic ClinVar variants found in the UBAP2L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-154225152-C-G		not specified	Uncertain significance (Dec 19, 2022)
1-154225154-C-T			Uncertain significance (Jan 06, 2023)
1-154225211-C-T		Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies	Pathogenic (Aug 30, 2023)
1-154234600-G-C		not specified	Uncertain significance (Mar 07, 2024)
1-154234661-A-G		not specified	Uncertain significance (Sep 15, 2021)
1-154234687-C-T		not specified	Uncertain significance (Sep 26, 2023)
1-154234705-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-154234714-G-C		not specified	Uncertain significance (Jun 01, 2023)
1-154236583-G-T		Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies	Pathogenic (Aug 30, 2023)
1-154236612-G-A		Neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies	Pathogenic (Aug 30, 2023)
1-154237043-T-A			Uncertain significance (Mar 27, 2023)
1-154237088-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-154243248-A-T		not specified	Uncertain significance (Feb 28, 2024)
1-154246295-C-A		not specified	Uncertain significance (Aug 14, 2023)
1-154246368-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-154251064-G-T		not specified	Uncertain significance (Jan 23, 2024)
1-154251157-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-154251328-C-A			Benign (Nov 20, 2018)
1-154251571-G-A		not specified	Uncertain significance (May 16, 2023)
1-154251607-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-154251633-C-G		not specified	Uncertain significance (Dec 09, 2023)
1-154253934-C-G		not specified	Uncertain significance (Mar 14, 2023)
1-154254081-C-T			Pathogenic (Oct 03, 2022)
1-154255167-C-T		not specified	Uncertain significance (Dec 20, 2022)
1-154255233-C-G		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBAP2L	protein_coding	protein_coding	ENST00000428931	26	51332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.20e-9	105021	0	2	105023	0.00000952

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.34	382	615	0.621	0.0000342	7012
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000528	0.0000528
European (Non-Finnish)	0.0000110	0.0000110
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.685
• ghis: 0.676

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubap2l
• Phenotype: growth/size/body region phenotype; reproductive system phenotype

Gene ontology

• Biological process: binding of sperm to zona pellucida;hematopoietic stem cell homeostasis
• Cellular component: nucleus;Ada2/Gcn5/Ada3 transcription activator complex;cytoplasm;PcG protein complex
• Molecular function: RNA binding;protein binding