USP6NL

USP6 N-terminal like

Basic information

Region (hg38): 10:11460510-11611666

Previous symbols: [ "USP6NL-IT1" ]

Links

ENSG00000148429 ∙ NCBI:9712 ∙ OMIM:605405 ∙ HGNC:16858 ∙ Uniprot:Q92738 ∙ 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 USP6NL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP6NL 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			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	3	0

Variants in USP6NL

This is a list of pathogenic ClinVar variants found in the USP6NL region.

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

Position	Type	Phenotype	Significance	ClinVar
10-11462505-G-A		not specified	Uncertain significance (Apr 03, 2023)
10-11462539-C-A		not specified	Uncertain significance (Oct 26, 2022)
10-11462548-C-T		not specified	Uncertain significance (Dec 19, 2022)
10-11462595-G-A		not specified	Uncertain significance (Feb 27, 2023)
10-11462602-C-T		not specified	Uncertain significance (Nov 07, 2023)
10-11462716-C-T		not specified	Uncertain significance (Dec 21, 2022)
10-11462812-C-T		not specified	Uncertain significance (Jan 26, 2023)
10-11462829-A-G		not specified	Uncertain significance (Aug 21, 2023)
10-11462861-G-C		not specified	Uncertain significance (Jun 28, 2022)
10-11462880-T-C		not specified	Uncertain significance (Oct 29, 2021)
10-11462884-C-G		not specified	Uncertain significance (Jan 30, 2024)
10-11462889-G-A		not specified	Uncertain significance (Jun 29, 2023)
10-11462934-T-C		not specified	Uncertain significance (May 26, 2023)
10-11463025-G-A		not specified	Uncertain significance (Aug 02, 2022)
10-11463057-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-11463106-G-C		not specified	Uncertain significance (Jan 04, 2024)
10-11463112-T-C		not specified	Uncertain significance (Jun 06, 2023)
10-11463172-G-A		not specified	Uncertain significance (Feb 03, 2022)
10-11463189-G-A		not specified	Uncertain significance (Dec 01, 2022)
10-11463204-T-C		not specified	Uncertain significance (Jan 22, 2024)
10-11463214-C-A		not specified	Uncertain significance (Jun 11, 2024)
10-11463246-C-T		not specified	Likely benign (Nov 01, 2021)
10-11463309-T-A		not specified	Uncertain significance (Feb 07, 2023)
10-11463315-T-A		not specified	Uncertain significance (Dec 22, 2023)
10-11463330-T-C		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP6NL	protein_coding	protein_coding	ENST00000277575	14	157809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.121	0.879	124583	0	59	124642	0.000237

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.146	468	459	1.02	0.0000272	5484
Missense in Polyphen		93	123.42	0.75351		1492
Synonymous	-0.876	202	187	1.08	0.0000127	1637
Loss of Function	4.43	10	40.3	0.248	0.00000246	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000856	0.000855
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000177
Middle Eastern	0.000111	0.000111
South Asian	0.000463	0.000458
Other	0.000179	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase-activating protein for RAB5A and RAB43. Involved in receptor trafficking. In complex with EPS8 inhibits internalization of EGFR. Involved in retrograde transport from the endocytic pathway to the Golgi apparatus. Involved in the transport of Shiga toxin from early and recycling endosomes to the trans-Golgi network. Required for structural integrity of the Golgi complex. {ECO:0000269|PubMed:11099046, ECO:0000269|PubMed:17562788, ECO:0000269|PubMed:17684057}.
• Pathway: EGF-EGFR Signaling Pathway;Vesicle-mediated transport;Membrane Trafficking;EGFR1;ErbB1 downstream signaling;PDGFR-beta signaling pathway;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.878
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.254
• hipred: Y
• hipred_score: 0.756
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.752

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp6nl

Gene ontology

• Biological process: intracellular protein transport;Golgi organization;virion assembly;retrograde transport, plasma membrane to Golgi;positive regulation of GTPase activity;plasma membrane to endosome transport;activation of GTPase activity;regulation of cilium assembly;regulation of Golgi organization
• Cellular component: cytosol;plasma membrane;cytoplasmic vesicle;trans-Golgi network membrane
• Molecular function: GTPase activator activity;Rab GTPase binding