UBQLN4

ubiquilin 4, the group of Ubiquilin family

Basic information

Region (hg38): 1:156035299-156053798

Previous symbols: [ "C1orf6" ]

Links

ENSG00000160803 ∙ NCBI:56893 ∙ OMIM:605440 ∙ HGNC:1237 ∙ Uniprot:Q9NRR5 ∙ 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 UBQLN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBQLN4 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				3	1	4
missense			18	1	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	18	4	3

Variants in UBQLN4

This is a list of pathogenic ClinVar variants found in the UBQLN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156037123-G-A		not specified	Uncertain significance (Apr 19, 2023)
1-156041545-G-A			Benign (Aug 28, 2018)
1-156041559-T-C		not specified	Likely benign (Sep 17, 2021)
1-156041579-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-156041596-G-A			Likely benign (May 01, 2022)
1-156041648-C-T		not specified	Uncertain significance (Jan 24, 2024)
1-156041653-T-C			Benign (Jun 20, 2018)
1-156041956-G-A		not specified	Uncertain significance (Feb 09, 2023)
1-156041978-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-156042212-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-156042789-G-A			Likely benign (May 14, 2018)
1-156042820-C-T		not specified	Uncertain significance (Aug 05, 2023)
1-156042909-C-A		not specified	Uncertain significance (Mar 20, 2023)
1-156044094-C-G		not specified	Uncertain significance (Jul 12, 2022)
1-156044111-G-A		not specified	Uncertain significance (Mar 19, 2024)
1-156044120-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-156044171-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-156044193-C-T		not specified	Uncertain significance (Mar 19, 2020)
1-156048508-C-T			Benign (Dec 31, 2019)
1-156050385-C-T		not specified	Uncertain significance (Jul 05, 2023)
1-156050510-G-A			Likely benign (May 01, 2022)
1-156051139-C-T		not specified	Uncertain significance (May 01, 2024)
1-156051154-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-156051181-C-T		not specified	Uncertain significance (Apr 13, 2023)
1-156051210-A-C		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBQLN4	protein_coding	protein_coding	ENST00000368309	11	18494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0175	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.88	196	347	0.565	0.0000198	3894
Missense in Polyphen		45	100.07	0.44969		1090
Synonymous	1.33	119	139	0.857	0.00000836	1249
Loss of Function	4.13	3	25.6	0.117	0.00000124	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000268	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of protein degradation via the ubiquitin-proteasome system (UPS). Mediates the proteasomal targeting of misfolded or accumulated proteins for degradation by binding (via UBA domain) to their polyubiquitin chains and by interacting (via ubiquitin-like domain) with the subunits of the proteasome (Ref. 6). Plays a role in the regulation of the proteasomal degradation of non-ubiquitinated GJA1 (By similarity). Acts as an adapter protein that recruits UBQLN1 to the autophagy machinery. Mediates the association of UBQLN1 with autophagosomes and the autophagy-related protein LC3 (MAP1LC3A/B/C) and may assist in the maturation of autophagosomes to autolysosomes by mediating autophagosome-lysosome fusion (PubMed:23459205). {ECO:0000250|UniProtKB:Q99NB8, ECO:0000269|PubMed:15280365, ECO:0000269|PubMed:23459205}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.174
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.271
• hipred: Y
• hipred_score: 0.825
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubqln4

Gene ontology

• Biological process: autophagy;regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of autophagosome maturation
• Cellular component: nucleus;cytoplasm;autophagosome;endoplasmic reticulum membrane;cytosol;cytoplasmic vesicle;nuclear proteasome complex;cytosolic proteasome complex;perinuclear region of cytoplasm
• Molecular function: protein binding;polyubiquitin modification-dependent protein binding;identical protein binding