MITD1

microtubule interacting and trafficking domain containing 1

Basic information

Region (hg38): 2:99161427-99181058

Links

ENSG00000158411 ∙ NCBI:129531 ∙ ∙ HGNC:25207 ∙ Uniprot:Q8WV92 ∙ 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 MITD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MITD1 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in MITD1

This is a list of pathogenic ClinVar variants found in the MITD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-99161677-GA-G			Benign (Oct 09, 2018)
2-99161958-A-T		LIPT1-related disorder	Benign/Likely benign (Dec 01, 2022)
2-99161959-T-C			Likely pathogenic (Oct 24, 2019)
2-99162014-C-T			Likely benign (Oct 04, 2023)
2-99162029-T-TA			Conflicting classifications of pathogenicity (Jun 14, 2022)
2-99162066-A-G			Uncertain significance (Nov 11, 2022)
2-99162066-A-T		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
2-99162078-G-A			Uncertain significance (Sep 27, 2022)
2-99162088-A-G		Lipoyl transferase 1 deficiency • Inborn genetic diseases	Likely pathogenic (Aug 05, 2022)
2-99162097-T-C			Uncertain significance (Aug 17, 2022)
2-99162107-G-T			Uncertain significance (Apr 25, 2023)
2-99162109-T-C			Uncertain significance (Aug 15, 2022)
2-99162141-A-G			Uncertain significance (Nov 23, 2021)
2-99162169-C-G		Inborn genetic diseases	Uncertain significance (Jan 05, 2022)
2-99162169-C-T		Lipoyl transferase 1 deficiency	Likely pathogenic (Jul 05, 2024)
2-99162249-C-G		Lipoyl transferase 1 deficiency	Conflicting classifications of pathogenicity (Oct 25, 2022)
2-99162250-G-A			Uncertain significance (Sep 13, 2017)
2-99162259-G-A		See cases	Uncertain significance (-)
2-99162272-A-G		not specified	Benign (Feb 01, 2024)
2-99162273-G-A		See cases • Lipoyl transferase 1 deficiency	Uncertain significance (-)
2-99162275-C-CT			Uncertain significance (Aug 16, 2022)
2-99162317-CA-C		not specified	Uncertain significance (Jan 25, 2024)
2-99162325-AG-A		Hypotonia;Abnormal optic nerve morphology;Abnormal cardiovascular system morphology;Failure to thrive;Hearing impairment • Lipoyl transferase 1 deficiency • not specified	Conflicting classifications of pathogenicity (Jan 22, 2024)
2-99162363-G-T			Uncertain significance (Sep 19, 2022)
2-99162398-G-T			Uncertain significance (Aug 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MITD1	protein_coding	protein_coding	ENST00000289359	7	19632

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000114	0.828	125699	0	45	125744	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.570	111	129	0.859	0.00000613	1637
Missense in Polyphen		25	34.906	0.7162		462
Synonymous	-0.209	48	46.2	1.04	0.00000228	444
Loss of Function	1.34	10	15.7	0.636	8.15e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000209
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000600	0.000598
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000115	0.000105
Middle Eastern	0.000600	0.000598
South Asian	0.000101	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient abscission at the end of cytokinesis, together with components of the ESCRT-III complex. {ECO:0000269|PubMed:23015756, ECO:0000269|PubMed:23045692}.

Recessive Scores

• pRec: 0.284

Intolerance Scores

• loftool: 0.588
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.626
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.667

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mitd1

Gene ontology

• Biological process: mitotic cytokinesis;negative regulation of protein binding;viral budding via host ESCRT complex;midbody abscission;multivesicular body sorting pathway
• Cellular component: extrinsic component of membrane;midbody;late endosome membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;protein domain specific binding;phosphatidylinositol binding;protein homodimerization activity