TMEM187

protein-coding

transmembrane protein 187, the group of MicroRNA protein coding host genes

Gene summary

This gene consists of two exons and encodes a multi-pass membrane protein. An alternatively spliced transcript variant encoding the same protein has been found, but its biological validity is not determined. [provided by RefSeq, May 2010]

Previous symbols:

CXorf12

MANE transcript

NM_003492.3

Inheritance

—

ClinVar variants

U:55B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chrX:153,972,754-153,983,194

External References & Databases

Ensembl (ENSG00000177854)

Transcript & Mutation Effects

hg38 • Region Span ~10.4 kb

Loading mutation effect viewer...

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 TMEM187 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003492.3. 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	2 clinvar	1 clinvar	4
missense			52 clinvar	7 clinvar	1 clinvar	60
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	9	2	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003492.3	RefSeq	NP_003483.1	1	MANE Select
ENST00000369982.5	Ensembl	ENSP00000358999.4	1	MANE Select
ENST00000425274.1	Ensembl	ENSP00000390108.1	1	Standard
ENST00000431598.1	Ensembl	ENSP00000412872.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

integral component of membrane
transport vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369982
Coding exons: 1
Length: 10869
Individuals with no LoFs: 125437
Homozygous LoFs: 9
Heterozygous LoFs: 13
Defined: 125459
p: 0.0000877

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.135	129	133	0.967	0.0000127	1654
Missense (PolyPhen)		30	35.527	0.84444		589
Synonymous	-0.194	72	69.9	1.03	0.00000732	585
Loss of Function	0.683	3	4.58	0.656	2.92e-7	59

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000077	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000076	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00014	rare
South Asian	0.00016	0.000098	rare
Other	0.00025	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.353
RVIS EVS: 0.02
RVIS percentile EVS: 55.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.475

Gene Damage Prediction

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