TMEM86A

transmembrane protein 86A

Basic information

Region (hg38): 11:18693122-18704785

Links

ENSG00000151117 ∙ NCBI:144110 ∙ ∙ HGNC:26890 ∙ Uniprot:Q8N2M4 ∙ 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 TMEM86A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM86A 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			7	1		8
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	9	1	0

Variants in TMEM86A

This is a list of pathogenic ClinVar variants found in the TMEM86A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18700981-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-18700999-C-A		not specified	Uncertain significance (Sep 28, 2022)
11-18701579-T-G		not specified	Uncertain significance (May 09, 2023)
11-18701612-C-T		not specified	Uncertain significance (Mar 19, 2024)
11-18701777-G-A		not specified	Uncertain significance (Sep 22, 2022)
11-18701782-C-T		not specified	Uncertain significance (Apr 28, 2022)
11-18701804-G-A		not specified	Uncertain significance (Jul 19, 2023)
11-18701841-C-G		not specified	Likely benign (Apr 07, 2023)
11-18701924-A-G		not specified	Uncertain significance (Nov 09, 2021)
11-18704503-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-18704529-T-C		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM86A	protein_coding	protein_coding	ENST00000280734	3	11664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0192	0.907	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.884	113	143	0.792	0.00000864	1522
Missense in Polyphen		38	58.467	0.64993		678
Synonymous	-0.402	66	62.0	1.06	0.00000400	531
Loss of Function	1.52	4	8.88	0.451	4.68e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000122
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.406
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.579
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0752

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem86a

Gene ontology

• Biological process: ether lipid metabolic process
• Cellular component: membrane;integral component of membrane
• Molecular function: alkenylglycerophosphocholine hydrolase activity;alkenylglycerophosphoethanolamine hydrolase activity