TROAP

trophinin associated protein

Basic information

Region (hg38): 12:49323236-49331731

Links

ENSG00000135451 ∙ NCBI:10024 ∙ OMIM:603872 ∙ HGNC:12327 ∙ Uniprot:Q12815 ∙ 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 TROAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TROAP 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		2
missense			48	6		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	48	8	0

Variants in TROAP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-49323646-G-A		not specified	Uncertain significance (May 08, 2024)
12-49323724-C-A		not specified	Uncertain significance (Sep 16, 2021)
12-49323879-G-A		not specified	Uncertain significance (Jan 24, 2024)
12-49323882-C-A		not specified	Uncertain significance (Apr 09, 2024)
12-49323923-C-G		not specified	Uncertain significance (Dec 07, 2023)
12-49323947-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-49323972-C-T		not specified	Uncertain significance (Jul 27, 2021)
12-49324032-A-G		not specified	Uncertain significance (Sep 13, 2023)
12-49325515-A-G		not specified	Uncertain significance (Aug 04, 2022)
12-49325565-G-T		not specified	Uncertain significance (Jan 16, 2024)
12-49325591-G-A		not specified	Uncertain significance (Feb 23, 2023)
12-49325753-C-T		not specified	Uncertain significance (Jul 12, 2023)
12-49325754-G-A		not specified	Uncertain significance (Feb 07, 2023)
12-49325793-G-A		not specified	Uncertain significance (Apr 19, 2023)
12-49325801-C-T			Likely benign (Feb 20, 2018)
12-49325847-G-A		not specified	Uncertain significance (Feb 10, 2022)
12-49326668-G-A		not specified	Likely benign (Mar 12, 2024)
12-49327231-A-T		not specified	Uncertain significance (Mar 25, 2024)
12-49327235-G-A		not specified	Uncertain significance (Apr 06, 2024)
12-49327242-T-C		not specified	Uncertain significance (Aug 14, 2023)
12-49327250-T-C		not specified	Uncertain significance (May 17, 2023)
12-49329017-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-49329206-C-T		not specified	Uncertain significance (Jul 14, 2021)
12-49329207-G-A		not specified	Likely benign (Nov 22, 2022)
12-49329219-T-C		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TROAP	protein_coding	protein_coding	ENST00000257909	14	8496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.51e-11	0.980	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.456	419	446	0.939	0.0000248	4884
Missense in Polyphen		105	111.59	0.94093		1339
Synonymous	0.914	159	174	0.912	0.00000908	1742
Loss of Function	2.33	23	38.7	0.595	0.00000220	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000491	0.000490
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved with bystin and trophinin in a cell adhesion molecule complex that mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of the embryo implantation.

Recessive Scores

• pRec: 0.0952

Intolerance Scores

• loftool: 0.186
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.5

Haploinsufficiency Scores

• pHI: 0.295
• hipred: N
• hipred_score: 0.199
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.759

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Troap

Gene ontology

• Biological process: cell adhesion
• Cellular component: cytoplasm
• Molecular function: protein binding