TRABD2A

TraB domain containing 2A

Basic information

Region (hg38): 2:84821650-84907008

Previous symbols: [ "C2orf89" ]

Links

ENSG00000186854 ∙ NCBI:129293 ∙ OMIM:614912 ∙ HGNC:27013 ∙ Uniprot:Q86V40 ∙ 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 TRABD2A gene.

• not_specified (72 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRABD2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001277053.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			65	7		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	7	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRABD2A	protein_coding	protein_coding	ENST00000335459	6	85359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-9	0.260	124609	0	47	124656	0.000189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.454	254	275	0.923	0.0000172	2917
Missense in Polyphen		80	96.101	0.83246		1169
Synonymous	0.359	104	109	0.956	0.00000608	948
Loss of Function	0.661	15	18.0	0.832	0.00000103	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000680	0.000679
Ashkenazi Jewish	0.00	0.00
East Asian	0.000458	0.000445
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000134	0.000133
Middle Eastern	0.000458	0.000445
South Asian	0.00	0.00
Other	0.000331	0.000330

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}.

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.198

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

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