MIS18A

MIS18 kinetochore protein A

Basic information

Region (hg38): 21:32268228-32279049

Previous symbols: [ "C21orf46", "C21orf45" ]

Links

ENSG00000159055 ∙ NCBI:54069 ∙ OMIM:618137 ∙ HGNC:1286 ∙ Uniprot:Q9NYP9 ∙ 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 MIS18A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIS18A 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			13	2		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	13	2	2

Variants in MIS18A

This is a list of pathogenic ClinVar variants found in the MIS18A region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32270455-A-G		not specified	Uncertain significance (Apr 27, 2024)
21-32270478-C-T			Benign (May 30, 2017)
21-32270480-C-T		not specified	Uncertain significance (Mar 31, 2024)
21-32270481-G-A			Benign (Jul 13, 2018)
21-32270495-G-C		not specified	Uncertain significance (Jan 09, 2024)
21-32270497-G-A		not specified	Uncertain significance (Oct 26, 2021)
21-32270514-C-A		not specified	Uncertain significance (Feb 22, 2023)
21-32270528-C-T		not specified	Likely benign (Jan 19, 2024)
21-32274833-C-A		not specified	Uncertain significance (Apr 04, 2023)
21-32274840-C-T		not specified	Uncertain significance (Dec 06, 2022)
21-32274849-G-A		not specified	Uncertain significance (Apr 20, 2024)
21-32278695-C-T		not specified	Uncertain significance (Sep 16, 2021)
21-32278699-T-C		not specified	Uncertain significance (Jul 06, 2021)
21-32278704-T-C		not specified	Uncertain significance (Jan 26, 2022)
21-32278794-G-A		not specified	Uncertain significance (Feb 03, 2022)
21-32278797-G-A		not specified	Uncertain significance (Jun 11, 2021)
21-32278816-C-T		not specified	Likely benign (Oct 10, 2023)
21-32278825-T-C		not specified	Uncertain significance (Oct 17, 2023)
21-32278843-C-T		not specified	Uncertain significance (Dec 27, 2023)
21-32278915-T-C		not specified	Uncertain significance (Mar 20, 2024)
21-32278998-G-A		not specified	Uncertain significance (Apr 15, 2024)
21-32279002-G-C		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIS18A	protein_coding	protein_coding	ENST00000290130	5	10851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00707	0.927	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.124	130	126	1.03	0.00000617	1510
Missense in Polyphen		25	37.888	0.65984		483
Synonymous	-0.382	56	52.5	1.07	0.00000267	424
Loss of Function	1.59	5	10.6	0.473	4.47e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000628	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000976	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for recruitment of CENPA to centromeres and normal chromosome segregation during mitosis. {ECO:0000269|PubMed:17199038}.
• Pathway: Nucleosome assembly;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.403
• hipred: Y
• hipred_score: 0.551
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mis18a
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype

Gene ontology

• Biological process: cell cycle;chromosome segregation;CENP-A containing nucleosome assembly;regulation of DNA methylation;cell division
• Cellular component: chromosome, centromeric region;chromatin;nucleus;nucleoplasm;cytosol
• Molecular function: protein binding;metal ion binding