MTCL1

microtubule crosslinking factor 1

Basic information

Region (hg38): 18:8705556-8832778

Previous symbols: [ "KIAA0802", "CCDC165", "SOGA2" ]

Links

ENSG00000168502

∙ NCBI:23255 ∙ OMIM:615766 ∙ HGNC:29121 ∙ Uniprot:Q9Y4B5 ∙ 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 MTCL1 gene.

Inborn_genetic_diseases (300 variants)
not_provided (21 variants)
not_specified (4 variants)
Cerebellar_ataxia (2 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Autosomal_dominant_cerebellar_ataxia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTCL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001395333.1. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				7 clinvar	3 clinvar	10
missense			269 clinvar	37 clinvar	3 clinvar	309
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	269	44	6

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTCL1	protein_coding	protein_coding	ENST00000359865	14	127118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000883	1.00	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.610	1043	989	1.05	0.0000664	10304
Missense in Polyphen		349	362.7	0.96223		3892
Synonymous	-1.45	462	424	1.09	0.0000291	3204
Loss of Function	5.16	20	64.8	0.309	0.00000373	702

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000316	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000290	0.000281
Middle Eastern	0.000220	0.000217
South Asian	0.000237	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Microtubule-associated factor involved in the late phase of epithelial polarization and microtubule dynamics regulation. Plays a role in the development and maintenance of non-centrosomal microtubule bundles at the lateral membrane in polarized epithelial cells. {ECO:0000269|PubMed:23902687}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

loftool
rvis_EVS: -1.3
rvis_percentile_EVS: 4.97

Haploinsufficiency Scores

pHI: 0.324
hipred: N
hipred_score: 0.422
ghis: 0.554

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Mtcl1
Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process: microtubule bundle formation;regulation of autophagy;establishment or maintenance of epithelial cell apical/basal polarity;positive regulation of protein targeting to membrane;positive regulation of microtubule motor activity
Cellular component: spindle pole;extracellular space;cytoplasm;cytoskeleton;apical plasma membrane;apicolateral plasma membrane;lateral plasma membrane;midbody;microtubule bundle
Molecular function: RNA binding;microtubule binding;protein homodimerization activity