TMUB2

transmembrane and ubiquitin like domain containing 2

Basic information

Region (hg38): 17:44186970-44191929

Links

ENSG00000168591 ∙ NCBI:79089 ∙ ∙ HGNC:28459 ∙ Uniprot:Q71RG4 ∙ 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 TMUB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMUB2 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		1
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in TMUB2

This is a list of pathogenic ClinVar variants found in the TMUB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44189105-C-T		not specified	Uncertain significance (Nov 07, 2022)
17-44189111-T-C		not specified	Uncertain significance (Feb 23, 2023)
17-44189216-C-A		not specified	Uncertain significance (Nov 14, 2023)
17-44189275-A-G		not specified	Uncertain significance (Jun 24, 2022)
17-44189276-C-A		not specified	Uncertain significance (Dec 03, 2021)
17-44189333-G-T		not specified	Uncertain significance (May 06, 2024)
17-44189396-T-C		not specified	Uncertain significance (Sep 17, 2021)
17-44189419-A-G		not specified	Uncertain significance (Apr 23, 2024)
17-44189474-A-G		not specified	Uncertain significance (Dec 07, 2023)
17-44189482-T-C		not specified	Uncertain significance (Nov 02, 2023)
17-44189501-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-44189512-G-A		not specified	Uncertain significance (Oct 25, 2023)
17-44189518-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-44189531-A-G		not specified	Uncertain significance (Jan 24, 2023)
17-44189539-G-A		not specified	Uncertain significance (Nov 09, 2023)
17-44189541-G-T		not specified	Uncertain significance (Aug 08, 2023)
17-44189566-G-A		not specified	Uncertain significance (Jun 10, 2024)
17-44189572-G-A		not specified	Uncertain significance (Jan 11, 2023)
17-44190571-C-T		not specified	Likely benign (Mar 06, 2023)
17-44190598-G-A		not specified	Uncertain significance (Nov 12, 2021)
17-44190684-G-A			Likely benign (Apr 01, 2023)
17-44190778-C-G		not specified	Uncertain significance (Mar 29, 2022)
17-44190800-C-T		not specified	Uncertain significance (Nov 08, 2021)
17-44190823-G-A		not specified	Uncertain significance (Aug 09, 2021)
17-44190826-T-G		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMUB2	protein_coding	protein_coding	ENST00000587989	3	4762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000141	0.416	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.324	206	193	1.07	0.0000107	2053
Missense in Polyphen		57	59.904	0.95153		701
Synonymous	-0.837	90	80.5	1.12	0.00000451	722
Loss of Function	0.397	8	9.31	0.860	4.81e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.709
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.392
• hipred: N
• hipred_score: 0.197
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmub2

Gene ontology

• Biological process: ubiquitin-dependent ERAD pathway
• Cellular component: integral component of membrane
• Molecular function: protein binding