TMEM87B

protein-coding

transmembrane protein 87B, the group of 7TM uncharacterized proteins

Gene summary

This gene encodes a protein that may interact with human papillomavirus type 18 E6 oncogene. The protein is also likely to be involved in endosome-to-trans-Golgi network retrograde transport. The gene is expressed in adult and fetal tissues, including brain and heart. This gene is a component of the 2q13 deletion syndrome. Mutations in this gene may be associated with congenital heart defects. [provided by RefSeq, Aug 2016]

MANE transcript

NM_032824.3

Inheritance

—

ClinVar variants

P:1U:63B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr2:112,055,269-112,119,318

External References & Databases

Ensembl (ENSG00000153214)

Transcript & Mutation Effects

hg38 • Region Span ~64.0 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 TMEM87B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032824.3. 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				1 clinvar		1
missense		1 clinvar	62 clinvar	6 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	63	7	0	71

Highest pathogenic variant AF is 0.000006815171

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032824.3	RefSeq	NP_116213.1	19	MANE Select
ENST00000283206.9	Ensembl	ENSP00000283206.4	19	MANE Select
NM_001329914.2	RefSeq	NP_001316843.1	19	Standard
ENST00000452614.6	Ensembl	ENSP00000393998.2	18	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
tmem87b	Danio rerio	Structure: aortic arch Quality: hypoplastic abnormal

Gene / Model

Organism

Observed Phenotype

tmem87b

Danio rerio

Structure: aortic arch

Quality: hypoplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

retrograde transport, endosome to Golgi

Cellular Component

Golgi membrane
cytosol
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000283206
Coding exons: 19
Length: 64096
Individuals with no LoFs: 125629
Homozygous LoFs: 1
Heterozygous LoFs: 118
Defined: 125748
p: 0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.681	251	283	0.886	0.0000138	3640
Missense (PolyPhen)		88	111.3	0.79063		1391
Synonymous	0.924	88	99.7	0.882	0.00000517	1003
Loss of Function	1.42	24	32.8	0.732	0.00000139	436

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00083	0.00082	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.0024	0.0023	notable
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in retrograde transport from endosomes to the trans-Golgi network (TGN). {ECO:0000269|PubMed:26157166}.;
Disease: DISEASE: Note=TMEM87B mutations may be involved in restrictive cardiomyopathy (RCM), a rare non-ischemic myocardial disease. RCM is characterized by restrictive ventricular-filling physiology in the presence of normal or reduced diastolic and/or systolic volumes (of 1 or both ventricles), biatrial enlargement, and normal ventricular wall thickness. {ECO:0000269|PubMed:27148590}.;

Recessive Scores

pRec: 0.0980

Intolerance Scores

LoFtool: 0.301
RVIS EVS: -0.89
RVIS percentile EVS: 10.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.437

Gene Damage Prediction

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