TMEM187

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

Basic information

Region (hg38): X:153972753-153983194

Previous symbols: [ "CXorf12" ]

Links

ENSG00000177854 ∙ NCBI:8269 ∙ OMIM:300059 ∙ HGNC:13705 ∙ Uniprot:Q14656 ∙ 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 TMEM187 gene.

• Inborn genetic diseases (24 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM187 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	1	3
missense			21	3	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	5	2

Variants in TMEM187

This is a list of pathogenic ClinVar variants found in the TMEM187 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-153982076-G-C		not specified	Likely benign (Oct 12, 2021)
X-153982096-G-C		not specified	Uncertain significance (Feb 10, 2022)
X-153982108-G-A		not specified	Likely benign (Apr 12, 2022)
X-153982139-G-T		not specified	Uncertain significance (Nov 22, 2021)
X-153982159-G-A		not specified	Uncertain significance (Sep 22, 2022)
X-153982159-G-C			Likely benign (Apr 11, 2018)
X-153982185-C-T			Likely benign (Apr 01, 2023)
X-153982190-C-T		not specified	Uncertain significance (Feb 17, 2022)
X-153982224-G-C		not specified	Uncertain significance (Nov 12, 2021)
X-153982226-C-T		not specified	Uncertain significance (May 25, 2022)
X-153982227-G-A			Likely benign (Jul 11, 2018)
X-153982249-G-A		not specified	Uncertain significance (Aug 31, 2022)
X-153982282-A-G		not specified	Uncertain significance (Nov 23, 2022)
X-153982349-A-G		not specified	Uncertain significance (Sep 01, 2021)
X-153982357-G-C		not specified	Uncertain significance (Jun 02, 2023)
X-153982369-C-T		not specified	Uncertain significance (Jul 09, 2021)
X-153982379-C-T		not specified	Uncertain significance (Feb 17, 2022)
X-153982391-G-A		not specified	Uncertain significance (Dec 15, 2022)
X-153982397-C-T		not specified	Uncertain significance (Mar 29, 2022)
X-153982475-G-A			Benign (Dec 20, 2018)
X-153982528-G-A		not specified	Conflicting classifications of pathogenicity (Oct 12, 2021)
X-153982567-G-A			Uncertain significance (Mar 01, 2024)
X-153982582-G-A		not specified	Uncertain significance (May 18, 2022)
X-153982595-C-T		not specified	Uncertain significance (Aug 15, 2023)
X-153982610-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM187	protein_coding	protein_coding	ENST00000369982	1	10869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0157	0.714	125437	9	13	125459	0.0000877

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.135	129	133	0.967	0.0000127	1654
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000774	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000762	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000141
Middle Eastern	0.0000762	0.0000544
South Asian	0.000157	0.0000980
Other	0.000250	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.353
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.201
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.475

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane;transport vesicle
• Molecular function: molecular_function