TPBG

trophoblast glycoprotein

Basic information

Region (hg38): 6:82363206-82367420

Links

ENSG00000146242 ∙ NCBI:7162 ∙ OMIM:190920 ∙ HGNC:12004 ∙ Uniprot:Q13641 ∙ 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 TPBG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPBG 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in TPBG

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

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

Position	Type	Phenotype	Significance	ClinVar
6-82364969-G-T		not specified	Uncertain significance (Mar 20, 2024)
6-82365058-T-C		not specified	Uncertain significance (Feb 23, 2023)
6-82365068-C-T		not specified	Uncertain significance (Sep 07, 2022)
6-82365073-G-A		not specified	Uncertain significance (May 25, 2022)
6-82365082-T-G		not specified	Uncertain significance (Jul 14, 2023)
6-82365089-C-A		not specified	Uncertain significance (May 03, 2023)
6-82365112-G-A		not specified	Uncertain significance (Nov 09, 2021)
6-82365131-C-G		not specified	Uncertain significance (Jun 12, 2023)
6-82365244-A-G		not specified	Uncertain significance (Jun 24, 2022)
6-82365309-GCTGGCGGAGCTGGCCGCGCTCAAC-G			Uncertain significance (Apr 16, 2021)
6-82365458-A-G		not specified	Uncertain significance (Aug 02, 2021)
6-82365580-C-G		not specified	Likely benign (May 21, 2024)
6-82365599-G-T		not specified	Uncertain significance (Dec 13, 2021)
6-82365632-A-C		not specified	Uncertain significance (Apr 01, 2024)
6-82365725-G-T		not specified	Uncertain significance (Feb 05, 2024)
6-82365772-A-C		not specified	Uncertain significance (Dec 19, 2023)
6-82365845-C-T		not specified	Uncertain significance (May 18, 2022)
6-82365914-A-G		not specified	Uncertain significance (Aug 08, 2022)
6-82365947-T-A		not specified	Uncertain significance (Feb 05, 2024)
6-82366072-C-T		not specified	Uncertain significance (Mar 31, 2024)
6-82366093-C-G		not specified	Uncertain significance (Nov 17, 2023)
6-82366097-A-G		not specified	Uncertain significance (Feb 28, 2024)
6-82366166-G-T		not specified	Uncertain significance (Dec 14, 2023)
6-82366189-A-G		not specified	Uncertain significance (Apr 01, 2024)
6-82366194-A-C		not specified	Uncertain significance (Jun 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPBG	protein_coding	protein_coding	ENST00000369750	1	7623

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0126	0.867	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0673	234	237	0.988	0.0000119	2670
Missense in Polyphen		51	74.984	0.68014		929
Synonymous	-3.51	155	109	1.43	0.00000560	934
Loss of Function	1.28	4	7.88	0.508	3.36e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000303	0.0000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an inhibitor of Wnt/beta-catenin signaling by indirectly interacting with LRP6 and blocking Wnt3a- dependent LRP6 internalization. {ECO:0000269|PubMed:22100263}.
• Pathway: EGF-Core (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.296
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.262
• hipred: N
• hipred_score: 0.272
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.880

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpbg
• 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); 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); cellular phenotype

Gene ontology

• Biological process: cell adhesion;positive regulation of synapse assembly
• Cellular component: endoplasmic reticulum;integral component of plasma membrane;cell surface