DSN1

DSN1 component of MIS12 kinetochore complex, the group of MIS12 kinetochore complex

Basic information

Region (hg38): 20:36751791-36773818

Previous symbols: [ "C20orf172" ]

Links

ENSG00000149636 ∙ NCBI:79980 ∙ OMIM:609175 ∙ HGNC:16165 ∙ Uniprot:Q9H410 ∙ 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 DSN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DSN1 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	2

Variants in DSN1

This is a list of pathogenic ClinVar variants found in the DSN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36752894-T-C		not specified	Uncertain significance (Jan 31, 2023)
20-36754779-C-A		not specified	Uncertain significance (Jul 20, 2022)
20-36754791-C-G		not specified	Uncertain significance (May 26, 2022)
20-36754830-T-C			Benign (Jun 18, 2018)
20-36755770-G-T		not specified	Uncertain significance (Aug 17, 2022)
20-36755800-A-C		not specified	Uncertain significance (Jul 14, 2021)
20-36758561-G-T		not specified	Uncertain significance (May 12, 2024)
20-36758570-T-G		not specified	Uncertain significance (Jan 20, 2023)
20-36758574-T-G		not specified	Uncertain significance (Jun 18, 2024)
20-36758589-A-T		not specified	Uncertain significance (Feb 21, 2024)
20-36762474-C-T		not specified	Uncertain significance (Sep 16, 2021)
20-36768033-C-T		not specified	Uncertain significance (Jan 16, 2024)
20-36770908-C-T		not specified	Uncertain significance (Sep 16, 2021)
20-36770917-G-A		not specified	Uncertain significance (Nov 22, 2021)
20-36770939-G-A		not specified	Uncertain significance (Jan 23, 2024)
20-36770945-A-G		not specified	Uncertain significance (Mar 21, 2023)
20-36771124-A-T		not specified	Uncertain significance (Mar 29, 2023)
20-36771127-A-G		not specified	Uncertain significance (Feb 17, 2023)
20-36771156-T-C			Benign (Jun 18, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DSN1	protein_coding	protein_coding	ENST00000426836	10	22028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.85e-8	0.753	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	162	188	0.861	0.00000973	2332
Missense in Polyphen		61	66.433	0.91822		851
Synonymous	1.03	55	65.6	0.838	0.00000329	649
Loss of Function	1.35	14	20.6	0.679	9.59e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000653	0.000652
Ashkenazi Jewish	0.000514	0.000496
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000400	0.000396
Middle Eastern	0.000163	0.000163
South Asian	0.0000727	0.0000653
Other	0.000331	0.000326

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:15502821, ECO:0000269|PubMed:16585270}.
• Pathway: Neutrophil degranulation;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;Innate Immune System;Immune System;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: 0.0779

Intolerance Scores

• loftool: 0.128
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.0823
• hipred: N
• hipred_score: 0.123
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.337

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dsn1

Gene ontology

• Biological process: mitotic sister chromatid segregation;neutrophil degranulation;cell division
• Cellular component: MIS12/MIND type complex;condensed chromosome kinetochore;nuclear MIS12/MIND complex;spindle pole;condensed nuclear chromosome inner kinetochore;fibrillar center;extracellular region;nucleus;nucleolus;cytosol;nuclear body;azurophil granule lumen
• Molecular function: protein binding