TDGF1

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	3 clinvar	5
missense			15 clinvar	3 clinvar	3 clinvar	21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	5	6	26

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
tdgf1	Danio rerio	Structure: hatching gland cell Quality: absent abnormal

Gene / Model

Organism

Observed Phenotype

tdgf1

Danio rerio

Structure: hatching gland cell

Quality: absent

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

signaling receptor binding
protein binding
growth factor activity
nodal binding
activin receptor binding

Cellular Component

extracellular region
extracellular space
plasma membrane
cell surface
apical plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296145
Coding exons: 6
Length: 51989
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0645	109	107	1.02	0.00000663	1227
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00083	0.00083	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00029	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.565

Intolerance Scores

LoFtool: 0.690
RVIS EVS: 0.24
RVIS percentile EVS: 69.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.105

Gene Damage Prediction

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