MISP

mitotic spindle positioning

Basic information

Region (hg38): 19:751112-764318

Previous symbols: [ "C19orf21" ]

Links

ENSG00000099812 ∙ NCBI:126353 ∙ OMIM:615289 ∙ HGNC:27000 ∙ Uniprot:Q8IVT2 ∙ 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 MISP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MISP 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	4	5
missense			77	7	5	89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	77	8	9

Variants in MISP

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

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

Position	Type	Phenotype	Significance	ClinVar
19-756953-C-T		not specified	Uncertain significance (Feb 13, 2024)
19-757014-T-C		not specified	Uncertain significance (Apr 25, 2023)
19-757023-A-G		not specified	Uncertain significance (Jan 05, 2022)
19-757037-T-C			Benign (Jun 29, 2018)
19-757052-A-G		not specified	Likely benign (Oct 12, 2021)
19-757127-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-757127-G-T		not specified	Uncertain significance (Jun 11, 2021)
19-757154-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-757188-G-A		not specified	Uncertain significance (Jun 10, 2022)
19-757225-G-C		not specified	Uncertain significance (Jul 06, 2021)
19-757229-T-G		not specified	Uncertain significance (Oct 26, 2022)
19-757259-G-A		not specified	Uncertain significance (Dec 13, 2023)
19-757280-C-T		not specified	Uncertain significance (Jun 12, 2023)
19-757320-G-T		not specified	Uncertain significance (Nov 09, 2023)
19-757321-C-T			Benign (Nov 18, 2017)
19-757354-G-A			Benign (Jul 23, 2018)
19-757367-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-757368-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-757373-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-757386-T-A		not specified	Uncertain significance (Apr 12, 2023)
19-757425-C-T		not specified	Uncertain significance (Jan 19, 2024)
19-757465-C-T			Benign (Mar 29, 2018)
19-757466-G-A		not specified	Uncertain significance (Nov 07, 2023)
19-757476-G-A		not specified	Likely benign (Feb 17, 2022)
19-757483-G-A			Benign (Jul 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MISP	protein_coding	protein_coding	ENST00000215582	4	13194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.31e-12	0.0978	125621	0	127	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.17	517	447	1.16	0.0000302	4315
Missense in Polyphen		150	124.08	1.2089		1248
Synonymous	-1.32	216	193	1.12	0.0000134	1448
Loss of Function	0.513	19	21.6	0.881	0.00000101	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000879	0.000848
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.0000545	0.0000544
Finnish	0.000430	0.000370
European (Non-Finnish)	0.000804	0.000774
Middle Eastern	0.0000545	0.0000544
South Asian	0.000184	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in mitotic spindle orientation and mitotic progression. Regulates the distribution of dynactin at the cell cortex in a PLK1-dependent manner, thus stabilizing cortical and astral microtubule attachments required for proper mitotic spindle positioning. May link microtubules to the actin cytospkeleton and focal adhesions. May be required for directed cell migration and centrosome orientation. May also be necessary for proper stacking of the Golgi apparatus. {ECO:0000269|PubMed:23509069, ECO:0000269|PubMed:23574715}.

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 50.58

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Misp

Gene ontology

• Biological process: cell cycle;cell division
• Cellular component: cytoskeleton;plasma membrane;focal adhesion;cell cortex;intracellular membrane-bounded organelle
• Molecular function: actin binding