UBBP4

ubiquitin B pseudogene 4

Basic information

Region (hg38): 17:22204093-22205009

Links

ENSG00000263563 ∙ NCBI:23666 ∙ ∙ HGNC:12467 ∙ ∙ ∙ 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 UBBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBBP4 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in UBBP4

This is a list of pathogenic ClinVar variants found in the UBBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-22204707-G-C			Likely benign (Apr 01, 2024)
17-22204923-T-C			Likely benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBBP4	protein_coding	protein_coding	ENST00000578713	2	2162

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000362	0.115	125332	3	413	125748	0.00166

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.41	179	133	1.34	0.00000820	1488
Missense in Polyphen		66	44.765	1.4744		544
Synonymous	-1.76	71	54.4	1.30	0.00000325	458
Loss of Function	-0.982	7	4.70	1.49	2.04e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000739	0.000725
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000220
Middle Eastern	0.000111	0.000109
South Asian	0.0122	0.0122
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.190
• ghis: 0.395

Gene Damage Prediction

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