NSL1

NSL1 component of MIS12 kinetochore complex, the group of MIS12 kinetochore complex

Basic information

Region (hg38): 1:212726153-212791782

Previous symbols: [ "C1orf48" ]

Links

ENSG00000117697 ∙ NCBI:25936 ∙ OMIM:609174 ∙ HGNC:24548 ∙ Uniprot:Q96IY1 ∙ 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 NSL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSL1 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					2	2
missense			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	2

Variants in NSL1

This is a list of pathogenic ClinVar variants found in the NSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-212738416-C-A		not specified	Uncertain significance (Dec 15, 2023)
1-212738436-C-T		not specified	Uncertain significance (Apr 01, 2024)
1-212738445-T-C		not specified	Uncertain significance (Feb 23, 2023)
1-212738461-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-212738574-T-A		not specified	Uncertain significance (Oct 08, 2024)
1-212738628-G-C		not specified	Uncertain significance (May 31, 2023)
1-212738677-C-T		not specified	Uncertain significance (Dec 06, 2022)
1-212739541-G-T		not specified	Uncertain significance (Oct 12, 2024)
1-212739549-G-C		not specified	Uncertain significance (Nov 25, 2024)
1-212739550-A-T		not specified	Uncertain significance (Nov 25, 2024)
1-212784430-C-T		not specified	Uncertain significance (Mar 30, 2024)
1-212791550-C-T		not specified	Uncertain significance (Sep 30, 2024)
1-212791552-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-212791560-A-C		not specified	Uncertain significance (May 11, 2022)
1-212791668-G-T			Benign (Feb 25, 2018)
1-212791670-G-A		not specified	Likely benign (Feb 13, 2024)
1-212791725-T-C			Benign (Feb 25, 2018)
1-212791726-G-T		not specified	Uncertain significance (Sep 22, 2022)
1-212791751-G-A		not specified	Likely benign (Jun 02, 2023)
1-212791757-C-T		not specified	Uncertain significance (Jul 15, 2021)
1-212791759-G-A		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSL1	protein_coding	protein_coding	ENST00000366977	6	65630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00393	0.962	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.244	144	152	0.944	0.00000689	1848
Missense in Polyphen		39	46.41	0.84034		610
Synonymous	-0.495	59	54.4	1.09	0.00000240	528
Loss of Function	1.85	6	13.3	0.451	5.70e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000331	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis. {ECO:0000269|PubMed:16585270}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.831
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.720
• ghis: 0.524

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsl1

Gene ontology

• Biological process: mitotic sister chromatid segregation;cell division
• Cellular component: MIS12/MIND type complex;condensed chromosome kinetochore;nucleoplasm;cytosol;nuclear speck
• Molecular function: protein binding