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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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

Variants in TWSG1

This is a list of pathogenic ClinVar variants found in the TWSG1 region.

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

Position	Phenotype	Significance	ClinVar
18-9359991-C-T	not specified	Uncertain significance (Jan 03, 2024)	3185086
18-9359992-G-A		Likely benign (Jan 01, 2023)	2648565
18-9360052-C-A	not specified	Uncertain significance (Oct 05, 2023)	3185087
18-9396508-C-T	not specified	Uncertain significance (Jul 14, 2023)	2611793
18-9399458-C-T		Likely benign (Jan 01, 2023)	2648566
18-9399520-T-C	not specified	Uncertain significance (Oct 06, 2023)	3185088

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
0.00611	0.915	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

loftool
rvis_EVS: -0.14
rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

pHI: 0.203
hipred: Y
hipred_score: 0.699
ghis: 0.602

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

Mouse Genome Informatics

Gene name: Twsg1
Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary phenotype;

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