ULBP2

UL16 binding protein 2

Basic information

Region (hg38): 6:149942013-149949235

Links

ENSG00000131015 ∙ NCBI:80328 ∙ OMIM:605698 ∙ HGNC:14894 ∙ Uniprot:Q9BZM5 ∙ 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 ULBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ULBP2 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				1		1
missense			17	1	2	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	2

Variants in ULBP2

This is a list of pathogenic ClinVar variants found in the ULBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149942131-C-T		not specified	Uncertain significance (Dec 15, 2021)
6-149945375-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-149945390-T-A		not specified	Uncertain significance (May 18, 2022)
6-149945440-C-G		not specified	Uncertain significance (Jul 11, 2023)
6-149945477-C-T		not specified	Uncertain significance (Oct 02, 2023)
6-149945498-C-G		not specified	Uncertain significance (Mar 15, 2024)
6-149945539-C-G		not specified	Uncertain significance (Mar 31, 2024)
6-149946451-C-T			Likely benign (Apr 10, 2018)
6-149946465-T-C		not specified	Uncertain significance (Oct 26, 2022)
6-149946494-T-C		not specified	Uncertain significance (Jun 07, 2023)
6-149946501-C-T		not specified	Uncertain significance (Jul 09, 2021)
6-149946519-G-A		not specified	Uncertain significance (Feb 10, 2022)
6-149946535-G-T		not specified	Uncertain significance (Dec 27, 2023)
6-149946552-T-C		not specified	Uncertain significance (Aug 29, 2022)
6-149946566-T-C		not specified	Likely benign (Aug 13, 2021)
6-149946584-G-A		not specified	Uncertain significance (Aug 16, 2022)
6-149946590-T-C		not specified	Uncertain significance (Nov 06, 2023)
6-149946591-G-A		not specified	Uncertain significance (Dec 06, 2022)
6-149946621-G-A		not specified	Uncertain significance (Dec 12, 2022)
6-149946641-C-A		not specified	Uncertain significance (Dec 08, 2023)
6-149947338-C-T			Benign (Jul 20, 2018)
6-149947356-G-A		not specified	Uncertain significance (Dec 31, 2023)
6-149947397-A-C			Benign (Jul 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ULBP2	protein_coding	protein_coding	ENST00000367351	4	7236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.84e-9	0.0361	125721	0	24	125745	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.36	168	125	1.34	0.00000639	1583
Missense in Polyphen		34	21.432	1.5864		333
Synonymous	-0.246	50	47.8	1.05	0.00000258	487
Loss of Function	-0.731	12	9.56	1.26	4.13e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00109	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00109	0.00109
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:11777960}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.317
• hipred: N
• hipred_score: 0.112
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.592

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ulbp1

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
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum;plasma membrane;external side of plasma membrane;cell surface;anchored component of plasma membrane
• Molecular function: protein binding;natural killer cell lectin-like receptor binding