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.

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.

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			25	4		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	0

Variants in TRABD2A

This is a list of pathogenic ClinVar variants found in the TRABD2A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-84821927-G-T		not specified	Uncertain significance (Jun 18, 2021)
2-84822020-G-A		not specified	Uncertain significance (Jul 30, 2023)
2-84822027-C-G		not specified	Uncertain significance (May 30, 2023)
2-84822029-C-T		not specified	Likely benign (Jun 16, 2023)
2-84822041-C-T		not specified	Likely benign (Jul 26, 2021)
2-84822095-A-G		not specified	Uncertain significance (May 28, 2024)
2-84823978-C-T		not specified	Uncertain significance (Apr 07, 2022)
2-84824013-C-T		not specified	Uncertain significance (May 07, 2024)
2-84824041-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-84824083-G-C		not specified	Uncertain significance (Jun 27, 2022)
2-84832080-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-84832083-G-A		not specified	Uncertain significance (May 25, 2022)
2-84839152-C-T		not specified	Uncertain significance (Aug 28, 2023)
2-84839203-T-C		not specified	Uncertain significance (Feb 28, 2023)
2-84839209-G-A		not specified	Uncertain significance (Aug 30, 2021)
2-84839247-C-T		not specified	Likely benign (Dec 15, 2023)
2-84839251-G-A		not specified	Uncertain significance (Jun 03, 2022)
2-84839301-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-84870243-A-C		not specified	Uncertain significance (Dec 18, 2023)
2-84870305-C-T		not specified	Uncertain significance (Oct 16, 2023)
2-84870347-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-84870402-C-G		not specified	Uncertain significance (Feb 09, 2023)
2-84870410-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-84870467-G-A		not specified	Uncertain significance (May 20, 2024)
2-84870529-C-T		not specified	Uncertain significance (Dec 12, 2023)

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