TMEM87B

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

Basic information

Region (hg38): 2:112055269-112119318

Links

ENSG00000153214 ∙ NCBI:84910 ∙ OMIM:617203 ∙ HGNC:25913 ∙ Uniprot:Q96K49 ∙ 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 TMEM87B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM87B 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				1		1
missense		1	32	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	32	4	0

Variants in TMEM87B

This is a list of pathogenic ClinVar variants found in the TMEM87B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112055601-G-T		not specified	Uncertain significance (Dec 07, 2021)
2-112055608-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-112055631-C-A		not specified	Uncertain significance (Jan 30, 2024)
2-112055658-G-C		not specified	Uncertain significance (Apr 23, 2024)
2-112055697-A-G		not specified	Likely benign (Nov 09, 2021)
2-112064185-C-A		not specified	Uncertain significance (Jun 22, 2023)
2-112064222-A-G		not specified	Uncertain significance (Jan 26, 2022)
2-112066951-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-112067003-G-T		not specified	Uncertain significance (May 17, 2023)
2-112067009-C-G		not specified	Uncertain significance (Dec 07, 2021)
2-112067012-C-A		not specified	Uncertain significance (May 31, 2023)
2-112077192-G-C		not specified	Uncertain significance (Dec 31, 2023)
2-112077217-A-T		not specified	Uncertain significance (Jun 29, 2022)
2-112077221-G-A			Likely benign (Jan 01, 2024)
2-112077256-A-G		not specified	Uncertain significance (Aug 14, 2023)
2-112081068-A-G		not specified	Uncertain significance (May 07, 2024)
2-112081335-T-C		not specified	Uncertain significance (Apr 07, 2023)
2-112081349-G-A		not specified	Uncertain significance (Apr 19, 2023)
2-112081353-A-G		not specified	Uncertain significance (May 17, 2023)
2-112081387-C-T		not specified	Likely benign (Jan 22, 2024)
2-112086053-C-T		not specified	Uncertain significance (May 25, 2022)
2-112086076-A-C		not specified	Uncertain significance (Jan 26, 2022)
2-112086077-T-C		not specified	Uncertain significance (Apr 11, 2023)
2-112089630-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-112089651-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM87B	protein_coding	protein_coding	ENST00000283206	19	64096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-13	0.487	125629	1	118	125748	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.681	251	283	0.886	0.0000138	3640
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000831	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000978	0.0000967
Middle Eastern	0.000831	0.000816
South Asian	0.00240	0.00226
Other	0.000501	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.196
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.437

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem87b

Zebrafish Information Network

• Gene name: tmem87b
• Affected structure: aortic arch
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: retrograde transport, endosome to Golgi
• Cellular component: Golgi membrane;cytosol;integral component of membrane