TMEM86B

transmembrane protein 86B

Basic information

Region (hg38): 19:55226638-55228784

Links

ENSG00000180089 ∙ NCBI:255043 ∙ OMIM:617806 ∙ HGNC:28448 ∙ Uniprot:Q8N661 ∙ 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 TMEM86B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM86B 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						0
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	20	3	0

Variants in TMEM86B

This is a list of pathogenic ClinVar variants found in the TMEM86B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55227201-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-55227203-C-G		not specified	Uncertain significance (May 13, 2024)
19-55227240-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-55227251-G-T		not specified	Uncertain significance (Dec 06, 2022)
19-55227267-G-A		not specified	Uncertain significance (May 03, 2023)
19-55227284-T-C		not specified	Uncertain significance (Aug 14, 2023)
19-55227309-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-55227342-A-G		not specified	Uncertain significance (Jun 24, 2022)
19-55227354-C-G		not specified	Uncertain significance (Aug 30, 2021)
19-55227354-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-55227369-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-55227371-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-55227383-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-55227411-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-55227413-G-A		not specified	Uncertain significance (Aug 12, 2022)
19-55227413-G-C		not specified	Uncertain significance (Oct 28, 2023)
19-55227543-C-T		not specified	Likely benign (Jul 09, 2021)
19-55227545-G-A		not specified	Uncertain significance (Apr 12, 2024)
19-55227852-C-T			Likely benign (Apr 01, 2023)
19-55228068-C-T			Likely benign (Apr 01, 2023)
19-55228197-C-T		not specified	Uncertain significance (May 14, 2024)
19-55228236-C-G		not specified	Uncertain significance (Jun 24, 2022)
19-55228277-C-T		not specified	Uncertain significance (Oct 20, 2023)
19-55228278-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-55228367-G-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM86B	protein_coding	protein_coding	ENST00000327042	3	3641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000507	0.138	125536	0	21	125557	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.576	148	130	1.14	0.00000794	1400
Missense in Polyphen		41	35.732	1.1474		469
Synonymous	-1.24	79	66.2	1.19	0.00000481	488
Loss of Function	-0.779	7	5.10	1.37	2.19e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000866	0.000860
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000529
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enzyme catalyzing the degradation of lysoplasmalogen. Lysoplasmalogens are formed by the hydrolysis of the abundant membrane glycerophospholipids plasmalogens. May control the respective levels of plasmalogens and lysoplasmalogens in cells and modulate cell membrane properties. {ECO:0000269|PubMed:21515882}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Acyl chain remodelling of PC;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.683
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.0875
• hipred: N
• hipred_score: 0.146
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem86b

Gene ontology

• Biological process: phosphatidylcholine acyl-chain remodeling;ether lipid metabolic process
• Cellular component: cytoplasm;endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: protein binding;ether hydrolase activity;alkenylglycerophosphocholine hydrolase activity;alkenylglycerophosphoethanolamine hydrolase activity