MTCL1

microtubule crosslinking factor 1

Basic information

Region (hg38): 18:8705555-8832778

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 (113 variants)
• not provided (18 variants)
• Autosomal dominant cerebellar ataxia (1 variants)
• not specified (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.

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				5	3	8
missense			102	17	3	122
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	102	23	6

Variants in MTCL1

This is a list of pathogenic ClinVar variants found in the MTCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-8706488-G-A		Cerebellar ataxia	Benign (May 04, 2023)
18-8718499-C-T		Cerebellar ataxia	Pathogenic (Jan 23, 2023)
18-8718526-G-A		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
18-8718580-A-G		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
18-8720429-G-A		Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
18-8720471-A-G		Inborn genetic diseases	Uncertain significance (Feb 06, 2024)
18-8783567-C-G		Inborn genetic diseases	Uncertain significance (Nov 05, 2021)
18-8783617-G-A		Inborn genetic diseases	Uncertain significance (Jan 12, 2024)
18-8783651-A-G		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
18-8783655-G-T		Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
18-8783728-G-A		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)
18-8783737-C-G		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
18-8783779-C-T		Inborn genetic diseases	Uncertain significance (Feb 01, 2022)
18-8783809-C-T		Autosomal dominant cerebellar ataxia	Uncertain significance (Nov 30, 2020)
18-8783840-G-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
18-8783855-G-A		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
18-8783864-C-G		Inborn genetic diseases	Uncertain significance (Nov 05, 2021)
18-8783864-C-T		Inborn genetic diseases	Likely benign (Feb 15, 2023)
18-8783869-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
18-8783904-C-T			Likely benign (Mar 29, 2018)
18-8783938-C-T		Inborn genetic diseases	Uncertain significance (Jul 15, 2021)
18-8783973-G-C		Inborn genetic diseases	Uncertain significance (May 23, 2023)
18-8783977-C-T		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
18-8783978-G-A		Inborn genetic diseases	Uncertain significance (May 27, 2022)
18-8784055-C-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)

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

• 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_gene_trap: N

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