TMUB1

transmembrane and ubiquitin like domain containing 1

Basic information

Region (hg38): 7:151081085-151083493

Previous symbols: [ "C7orf21" ]

Links

ENSG00000164897 ∙ NCBI:83590 ∙ OMIM:614792 ∙ HGNC:21709 ∙ Uniprot:Q9BVT8 ∙ 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 TMUB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMUB1 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in TMUB1

This is a list of pathogenic ClinVar variants found in the TMUB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-151081596-A-G		not specified	Uncertain significance (Sep 16, 2021)
7-151081616-G-A		not specified	Uncertain significance (Mar 16, 2024)
7-151081638-G-A		not specified	Uncertain significance (May 28, 2023)
7-151081643-T-G		not specified	Uncertain significance (Feb 02, 2024)
7-151081655-T-C		not specified	Uncertain significance (Dec 06, 2022)
7-151081721-G-A		not specified	Uncertain significance (Nov 14, 2023)
7-151081736-C-T		not specified	Uncertain significance (Nov 28, 2023)
7-151081748-G-C		not specified	Uncertain significance (May 09, 2022)
7-151081886-C-T		not specified	Uncertain significance (Dec 02, 2021)
7-151082238-A-T		not specified	Uncertain significance (Nov 29, 2023)
7-151082277-G-A		not specified	Uncertain significance (Oct 12, 2021)
7-151082295-G-A		not specified	Uncertain significance (Apr 29, 2024)
7-151082356-C-T		not specified	Uncertain significance (Jul 26, 2021)
7-151082367-G-A		not specified	Likely benign (Dec 19, 2022)
7-151082455-C-T		not specified	Uncertain significance (Aug 02, 2021)
7-151082472-G-A		not specified	Uncertain significance (Mar 19, 2024)
7-151082484-G-A		not specified	Uncertain significance (Jan 30, 2024)
7-151082485-C-A		not specified	Uncertain significance (Jan 30, 2024)
7-151082490-G-A		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMUB1	protein_coding	protein_coding	ENST00000392818	2	2467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0367	0.843	125656	0	6	125662	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.803	103	129	0.801	0.00000773	1506
Missense in Polyphen		46	63.679	0.72238		801
Synonymous	0.821	58	66.5	0.872	0.00000449	574
Loss of Function	1.25	3	6.40	0.469	3.35e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000611	0.0000611
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000105	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000699	0.0000653
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in sterol-regulated ubiquitination and degradation of HMG-CoA reductase HMGCR (PubMed:21343306). Involved in positive regulation of AMPA-selective glutamate receptor GRIA2 recycling to the cell surface (By similarity). Acts as negative regulator of hepatocyte growth during regeneration (By similarity). {ECO:0000250|UniProtKB:Q53AQ4, ECO:0000250|UniProtKB:Q9JMG3, ECO:0000269|PubMed:21343306}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.358
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.200
• hipred: Y
• hipred_score: 0.625
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmub1
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: ubiquitin-dependent ERAD pathway
• Cellular component: nucleoplasm;nucleolus;microtubule organizing center;cytosol;integral component of membrane;cell junction;postsynaptic membrane;recycling endosome
• Molecular function: protein binding