NSFL1C

NSFL1 cofactor, the group of UBX domain containing

Basic information

Region (hg38): 20:1442161-1473842

Links

ENSG00000088833 ∙ NCBI:55968 ∙ OMIM:606610 ∙ HGNC:15912 ∙ Uniprot:Q9UNZ2 ∙ 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 NSFL1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSFL1C 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		18
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	1	1

Variants in NSFL1C

This is a list of pathogenic ClinVar variants found in the NSFL1C region.

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

Position	Type	Phenotype	Significance	ClinVar
20-1443777-T-C		not specified	Uncertain significance (Jan 16, 2024)
20-1443894-A-T		not specified	Uncertain significance (Nov 08, 2022)
20-1445696-C-T		not specified	Uncertain significance (Dec 27, 2022)
20-1452596-C-T		not specified	Uncertain significance (Jan 30, 2024)
20-1452599-G-C		not specified	Uncertain significance (Dec 02, 2021)
20-1452614-G-A			Likely benign (Oct 01, 2022)
20-1453037-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-1453062-T-C		not specified	Uncertain significance (Nov 03, 2022)
20-1454971-G-T		not specified	Uncertain significance (Jun 11, 2021)
20-1454972-G-T		not specified	Uncertain significance (Oct 29, 2021)
20-1454978-T-G		not specified	Uncertain significance (Dec 21, 2022)
20-1454990-G-T		not specified	Uncertain significance (Jan 03, 2024)
20-1455004-C-T		not specified	Uncertain significance (Dec 05, 2022)
20-1455062-C-T		not specified	Uncertain significance (Dec 21, 2023)
20-1455063-G-C		not specified	Uncertain significance (Jan 31, 2022)
20-1464341-C-T		not specified	Uncertain significance (May 26, 2024)
20-1464352-T-C			Benign (Dec 31, 2019)
20-1464381-C-G		not specified	Uncertain significance (Jun 18, 2021)
20-1466740-A-G		not specified	Uncertain significance (Mar 23, 2023)
20-1466755-G-A		not specified	Uncertain significance (Dec 06, 2021)
20-1466788-C-G		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSFL1C	protein_coding	protein_coding	ENST00000476071	10	31681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0495	0.950	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	154	214	0.719	0.0000119	2430
Missense in Polyphen		53	87.071	0.6087		981
Synonymous	-0.139	87	85.4	1.02	0.00000511	724
Loss of Function	2.92	6	20.1	0.298	0.00000102	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.000296	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reduces the ATPase activity of VCP (By similarity). Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis (By similarity). May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER) (By similarity). Inhibits the activity of CTSL (in vitro) (PubMed:15498563). Together with UBXN2B/p37, regulates the centrosomal levels of kinase AURKA/Aurora A during mitotic progression by promoting AURKA removal from centrosomes in prophase (PubMed:23649807). Also, regulates spindle orientation during mitosis (PubMed:23649807). {ECO:0000250|UniProtKB:O35987, ECO:0000269|PubMed:15498563, ECO:0000269|PubMed:23649807}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.731
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.745
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsfl1c

Gene ontology

• Biological process: autophagosome assembly;establishment of mitotic spindle orientation;Golgi organization;nuclear envelope reassembly;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of mitotic centrosome separation;membrane fusion;negative regulation of protein localization to centrosome
• Cellular component: nucleoplasm;chromosome;Golgi stack;cytosol;plasma membrane;spindle pole centrosome;intermediate filament cytoskeleton;VCP-NSFL1C complex
• Molecular function: protein binding;phospholipid binding;ubiquitin binding;ATPase binding