TRO

trophinin, the group of Small nucleolar RNA protein coding host genes|MAGE family

Basic information

Region (hg38): X:54920462-54931431

Links

ENSG00000067445 ∙ NCBI:7216 ∙ OMIM:300132 ∙ HGNC:12326 ∙ Uniprot:Q12816 ∙ 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 TRO gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRO 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				4	1	5
missense			45	9		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	45	13	1

Variants in TRO

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

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

Position	Type	Phenotype	Significance	ClinVar
X-54922268-G-A		not specified	Uncertain significance (Sep 26, 2023)
X-54922594-C-G		not specified	Uncertain significance (Aug 16, 2022)
X-54922594-C-T		not specified	Uncertain significance (Dec 08, 2023)
X-54922738-G-A		not specified	Uncertain significance (Nov 21, 2022)
X-54922846-A-C		not specified	Uncertain significance (May 18, 2023)
X-54922878-A-G		not specified	Uncertain significance (Dec 03, 2021)
X-54922914-C-G		not specified	Uncertain significance (Dec 06, 2021)
X-54922917-G-A		not specified	Uncertain significance (Sep 06, 2022)
X-54922961-G-A			Likely benign (Oct 01, 2022)
X-54922980-G-A		not specified	Uncertain significance (Mar 29, 2023)
X-54923082-G-A		not specified	Uncertain significance (Feb 27, 2023)
X-54923088-A-G		not specified	Uncertain significance (Apr 29, 2024)
X-54923136-C-G		not specified	Uncertain significance (Aug 02, 2023)
X-54923200-C-T		not specified	Uncertain significance (May 27, 2022)
X-54923415-A-C		not specified	Uncertain significance (Dec 07, 2021)
X-54923417-C-G		not specified	Uncertain significance (Jan 10, 2023)
X-54923422-C-T		not specified	Uncertain significance (Apr 07, 2022)
X-54923445-G-T		not specified	Uncertain significance (Oct 12, 2022)
X-54923539-G-A		not specified	Uncertain significance (Feb 28, 2023)
X-54923605-C-T		not specified	Uncertain significance (Mar 19, 2024)
X-54923700-G-A		not specified	Uncertain significance (Nov 07, 2022)
X-54924512-G-A		not specified	Uncertain significance (May 06, 2024)
X-54924527-C-T			Likely benign (Sep 01, 2022)
X-54924674-A-G		not specified	Uncertain significance (Mar 18, 2024)
X-54924677-A-T		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRO	protein_coding	protein_coding	ENST00000173898	11	10970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000385	0.990	125732	2	11	125745	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	481	550	0.875	0.0000403	9436
Missense in Polyphen		64	94.78	0.67525		1848
Synonymous	0.605	201	212	0.947	0.0000166	3044
Loss of Function	2.30	11	22.9	0.480	0.00000180	405

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000221
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000163
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000499	0.0000352
Middle Eastern	0.000224	0.000163
South Asian	0.00	0.00
Other	0.000225	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved with bystin and tastin 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. Directly responsible for homophilic cell adhesion.

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.585
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.25

Haploinsufficiency Scores

• pHI: 0.445
• hipred: N
• hipred_score: 0.229
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tro
• 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); normal phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;embryo implantation
• Cellular component: intrinsic component of plasma membrane
• Molecular function: protein binding