TDGF1

teratocarcinoma-derived growth factor 1

Basic information

Region (hg38): 3:46574533-46582457

Links

ENSG00000241186 ∙ NCBI:6997 ∙ OMIM:187395 ∙ HGNC:11701 ∙ Uniprot:P13385 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Forebrain anomalies; Congenital cardiac malformations	AD	Cardiovascular	The condition can include congenital cardiac anomalies, and awareness may allow early identification and management	Craniofacial; Cardiovascular; Endocrine; Neurologic	12073012; 18538293
Individuals with forebrain anomalies such as holoprosencephaly may demonstrate endocrine anomalies, including diabetes insipidus

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TDGF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TDGF1 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	3	5
missense			10	3	3	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				13	7	20
Total	0	0	10	18	13

Variants in TDGF1

This is a list of pathogenic ClinVar variants found in the TDGF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-46577270-A-C			Benign (Nov 27, 2018)
3-46577748-T-A			Benign (Jan 19, 2019)
3-46577992-G-A		not specified	Uncertain significance (Jun 05, 2024)
3-46578042-C-T			Benign (Feb 02, 2019)
3-46578064-G-A			Likely benign (Sep 29, 2019)
3-46578125-C-G			Likely benign (Sep 29, 2019)
3-46578283-G-A			Likely benign (Sep 29, 2019)
3-46578784-T-A			Benign (Feb 02, 2019)
3-46579028-T-C			Likely benign (Sep 29, 2019)
3-46579072-C-T			Likely benign (Jan 09, 2019)
3-46579104-G-T		not specified	Uncertain significance (Jan 03, 2024)
3-46579114-A-T		not specified	Likely benign (Feb 07, 2023)
3-46579124-T-C			Benign (Nov 27, 2018)
3-46579155-A-G			Likely benign (May 03, 2018)
3-46579258-C-A		CRIPTO-related disorder	Uncertain significance (Apr 13, 2023)
3-46579265-G-A		not specified	Likely benign (Dec 03, 2021)
3-46579267-G-A		not specified	Uncertain significance (Aug 10, 2024)
3-46579270-T-G			Benign (Sep 29, 2019)
3-46579285-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-46579311-G-A			Benign (Sep 29, 2019)
3-46579322-G-A		not specified	Uncertain significance (May 04, 2023)
3-46579328-G-C			Uncertain significance (Feb 28, 2023)
3-46579409-T-A			Benign (Sep 29, 2019)
3-46579471-T-G			Likely benign (Sep 29, 2019)
3-46579567-A-G			Likely benign (Sep 29, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TDGF1	protein_coding	protein_coding	ENST00000296145	6	51989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.16e-11	0.0120	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0645	109	107	1.02	0.00000663	1227
Missense in Polyphen		18	18.934	0.95066		253
Synonymous	-0.512	43	38.9	1.10	0.00000225	369
Loss of Function	-1.28	13	8.90	1.46	3.91e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000831	0.000832
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.000294	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GPI-anchored cell membrane protein involved in Nodal signaling. Cell-associated TDGF1 acts as a Nodal coreceptor in cis. Shedding of TDGF1 by TMEM8A modulates Nodal signaling by allowing soluble TDGF1 to act as a Nodal coreceptor on other cells (PubMed:27881714). Could play a role in the determination of the epiblastic cells that subsequently give rise to the mesoderm (PubMed:11909953). {ECO:0000269|PubMed:11909953, ECO:0000269|PubMed:27881714}.
• Pathway: POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Developmental Biology;Regulation of signaling by NODAL;Signaling by NODAL;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Transcriptional regulation of pluripotent stem cells;Glypican 1 network (Consensus)

Recessive Scores

• pRec: 0.565

Intolerance Scores

• loftool: 0.690
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.221

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tdgf1
• Phenotype: cellular 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); vision/eye phenotype; embryo phenotype; 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); 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); normal phenotype

Zebrafish Information Network

• Gene name: tdgf1
• Affected structure: hatching gland cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: activation of MAPK activity;morphogenesis of a branching structure;cell migration involved in sprouting angiogenesis;epidermal growth factor receptor signaling pathway;determination of left/right symmetry;heart development;positive regulation of cell population proliferation;anterior/posterior axis specification, embryo;embryo development ending in birth or egg hatching;anterior/posterior pattern specification;regulation of signal transduction;regulation of signaling receptor activity;positive regulation of endothelial cell migration;peptidyl-serine phosphorylation;cell differentiation;positive regulation of cell migration;BMP signaling pathway;mammary gland development;somatic stem cell population maintenance;cellular response to hepatocyte growth factor stimulus;nodal signaling pathway;negative regulation of apoptotic process;cellular response to fibroblast growth factor stimulus;anatomical structure development;positive regulation of peptidyl-tyrosine phosphorylation;cellular response to interferon-gamma;cellular response to interleukin-6;cellular response to tumor necrosis factor;cellular response to epidermal growth factor stimulus
• Cellular component: extracellular region;extracellular space;plasma membrane;cell surface;apical plasma membrane;extrinsic component of plasma membrane;anchored component of membrane;membrane raft
• Molecular function: signaling receptor binding;protein binding;growth factor activity;nodal binding;activin receptor binding