TRO

protein-coding

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

Gene summary

This gene encodes a membrane protein that mediates cell adhesion between trophoblastic cells and the epithelial cells of the endometrium. The encoded protein participates in cell signalling during embryo implantation, and may also be involved in cancer formation. This gene is located near several other closely related genes on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]

MANE transcript

NM_001039705.3

Inheritance

—

ClinVar variants

U:209B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chrX:54,920,462-54,931,431

External References & Databases

Ensembl (ENSG00000067445)

Transcript & Mutation Effects

hg38 • Region Span ~11.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRO variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 148

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039705.3. Only rare variants are included.

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			20 clinvar	5 clinvar	1 clinvar	26
missense			175 clinvar	14 clinvar		189
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	0	209	19	1	229

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039705.3	RefSeq	NP_001034794.1	11	MANE Select
ENST00000173898.12	Ensembl	ENSP00000173898.7	11	MANE Select
NM_001271183.2	RefSeq	NP_001258112.1	7	Standard
NM_001271184.2	RefSeq	NP_001258113.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

homophilic cell adhesion via plasma membrane adhesion molecules
embryo implantation

Molecular Function

protein binding

Cellular Component

intrinsic component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000173898
Coding exons: 11
Length: 10970
Individuals with no LoFs: 125732
Homozygous LoFs: 2
Heterozygous LoFs: 11
Defined: 125745
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	481	550	0.875	0.0000403	9436
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00018	rare
Latino/Admixed American	0.000037	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00016	rare
Finnish	0.000062	0.000046	rare
European (Non-Finnish)	0.000050	0.000035	rare
South Asian	0	0.0	absent
Other	0.00023	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.373

Gene Damage Prediction

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