ULBP3

UL16 binding protein 3

Basic information

Region (hg38): 6:150061053-150069121

Links

ENSG00000131019 ∙ NCBI:79465 ∙ OMIM:605699 ∙ HGNC:14895 ∙ Uniprot:Q9BZM4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ULBP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ULBP3 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						0
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in ULBP3

This is a list of pathogenic ClinVar variants found in the ULBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-150064672-T-C		not specified	Uncertain significance (May 26, 2024)
6-150064701-A-G		not specified	Uncertain significance (Feb 22, 2023)
6-150065446-A-C		not specified	Uncertain significance (Dec 04, 2024)
6-150065447-G-C		not specified	Uncertain significance (Dec 04, 2024)
6-150065524-G-A		not specified	Uncertain significance (Jul 05, 2024)
6-150065556-C-T		not specified	Uncertain significance (Jun 16, 2023)
6-150065577-A-T		not specified	Uncertain significance (Dec 15, 2023)
6-150065587-G-A		not specified	Uncertain significance (Sep 01, 2021)
6-150065617-G-A		not specified	Uncertain significance (Apr 05, 2023)
6-150065620-T-G		not specified	Uncertain significance (Sep 24, 2024)
6-150065629-C-T		not specified	Uncertain significance (May 25, 2023)
6-150065658-T-C		not specified	Uncertain significance (Feb 21, 2024)
6-150065916-T-A		not specified	Uncertain significance (Apr 19, 2023)
6-150065985-C-T		not specified	Likely benign (Sep 16, 2021)
6-150065991-G-A		not specified	Uncertain significance (Oct 21, 2024)
6-150065998-T-A		not specified	Uncertain significance (Sep 13, 2023)
6-150066001-C-T		not specified	Uncertain significance (Dec 19, 2023)
6-150066019-G-T		not specified	Uncertain significance (Oct 13, 2023)
6-150066030-G-T		not specified	Uncertain significance (Oct 01, 2024)
6-150068990-G-A		not specified	Uncertain significance (Jun 28, 2022)
6-150069035-G-A		not specified	Likely benign (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ULBP3	protein_coding	protein_coding	ENST00000367339	4	5946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.74e-11	0.0157	125726	0	3	125729	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.439	148	134	1.11	0.00000676	1607
Missense in Polyphen		31	33.575	0.92332		487
Synonymous	0.0293	52	52.3	0.995	0.00000270	466
Loss of Function	-0.892	14	10.8	1.29	4.70e-7	126

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	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds and activates the KLRK1/NKG2D receptor, mediating natural killer cell cytotoxicity. {ECO:0000269|PubMed:11491531, ECO:0000269|PubMed:11754823, ECO:0000269|PubMed:11777960}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.837
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.1

Haploinsufficiency Scores

• pHI: 0.0515
• hipred: N
• hipred_score: 0.139
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0631

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 9230019H11Rik

Gene ontology

• Biological process: T cell mediated cytotoxicity;immune response;viral process;natural killer cell activation;natural killer cell mediated cytotoxicity;susceptibility to natural killer cell mediated cytotoxicity;regulation of immune response
• Cellular component: extracellular space;plasma membrane;external side of plasma membrane;anchored component of plasma membrane
• Molecular function: protein binding;natural killer cell lectin-like receptor binding