TWSG1

twisted gastrulation BMP signaling modulator 1

Basic information

Region (hg38): 18:9334767-9402420

Links

ENSG00000128791 ∙ NCBI:57045 ∙ OMIM:605049 ∙ HGNC:12429 ∙ Uniprot:Q9GZX9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 10.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_020648.6	NP_065699.1	4	yes	-
ENST00000262120.10	ENSP00000262120.5	4	yes	-
ENST00000581641.1	ENSP00000464458.1	3	-	-
ENST00000583147.5	ENSP00000463331.1	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TWSG1 gene.

• not_specified (24 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TWSG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_020648.6. 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			1	2		3
missense			24			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	28	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TWSG1	protein_coding	protein_coding	ENST00000262120	4	67654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.951	97	127	0.763	0.00000644	1490
Missense in Polyphen		32	39.696	0.80613		459
Synonymous	0.0150	44	44.1	0.997	0.00000240	395
Loss of Function	1.51	5	10.2	0.490	4.95e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000467	0.000467
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000286	0.000277
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000326	0.000326
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in dorsoventral axis formation. Seems to antagonize BMP signaling by forming ternary complexes with CHRD and BMPs, thereby preventing BMPs from binding to their receptors. In addition to the anti-BMP function, also has pro-BMP activity, partly mediated by cleavage and degradation of CHRD, which releases BMPs from ternary complexes. May be an important modulator of BMP-regulated cartilage development and chondrocyte differentiation. May play a role in thymocyte development (By similarity). {ECO:0000250}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.309

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: twsg1b
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: ossification;mesoderm formation;negative regulation of cytokine production;transforming growth factor beta receptor signaling pathway;salivary gland morphogenesis;positive regulation of pathway-restricted SMAD protein phosphorylation;hemopoiesis;cell differentiation;BMP signaling pathway;positive regulation of BMP signaling pathway;negative regulation of BMP signaling pathway;forebrain development;camera-type eye development;negative regulation of osteoblast differentiation;negative regulation of CD4-positive, alpha-beta T cell activation;negative regulation of CD4-positive, alpha-beta T cell proliferation
• Cellular component: extracellular space
• Molecular function: protein binding;transforming growth factor beta binding