TRABD2B

TraB domain containing 2B

Basic information

Region (hg38): 1:47760528-47997385

Links

ENSG00000269113 ∙ NCBI:388630 ∙ OMIM:614913 ∙ HGNC:44200 ∙ Uniprot:A6NFA1 ∙ 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 TRABD2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRABD2B 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	0

Variants in TRABD2B

This is a list of pathogenic ClinVar variants found in the TRABD2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-47775212-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-47775251-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-47775269-T-A		not specified	Uncertain significance (Mar 15, 2024)
1-47775275-A-G		not specified	Uncertain significance (May 31, 2024)
1-47775276-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-47775321-C-T		not specified	Uncertain significance (Aug 14, 2023)
1-47775357-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-47775377-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-47775411-G-A		not specified	Uncertain significance (May 09, 2024)
1-47775428-T-C		not specified	Likely benign (May 24, 2023)
1-47778458-G-T		not specified	Uncertain significance (Oct 14, 2023)
1-47778521-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-47794589-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-47794680-C-G		not specified	Uncertain significance (Jun 17, 2024)
1-47794724-C-G		not specified	Uncertain significance (Oct 27, 2023)
1-47794724-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-47801502-C-A		not specified	Uncertain significance (Jan 29, 2024)
1-47994169-G-T		not specified	Uncertain significance (Apr 12, 2024)
1-47994204-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-47994267-G-A		not specified	Uncertain significance (Jan 06, 2023)
1-47994276-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-47994314-T-C		not specified	Uncertain significance (Aug 16, 2022)
1-47994385-G-A			Likely benign (Apr 01, 2023)
1-47994416-G-A		not specified	Uncertain significance (Aug 30, 2021)
1-47994458-C-T		not specified	Likely benign (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRABD2B	protein_coding	protein_coding	ENST00000606738	7	236368

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.843	0.157	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.99	123	258	0.477	0.0000164	3308
Missense in Polyphen		39	103.44	0.37701		1139
Synonymous	1.52	93	114	0.818	0.00000781	1068
Loss of Function	3.09	2	14.9	0.135	6.37e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloprotease that acts as a negative regulator of the Wnt signaling pathway by mediating the cleavage of the 8 N- terminal residues of a subset of Wnt proteins. Following cleavage, Wnt proteins become oxidized and form large disulfide-bond oligomers, leading to their inactivation. Able to cleave WNT3A, WNT5, but not WNT11. Required for head formation. {ECO:0000269|PubMed:22726442}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.279
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trabd2b

Gene ontology

• Biological process: proteolysis;Wnt signaling pathway;negative regulation of Wnt signaling pathway;positive regulation of protein oligomerization;positive regulation of protein oxidation
• Cellular component: integral component of plasma membrane;membrane;integral component of organelle membrane
• Molecular function: metalloendopeptidase activity;protein binding;Wnt-protein binding;metal ion binding