TMEM218

transmembrane protein 218

Basic information

Region (hg38): 11:125094389-125111763

Links

ENSG00000150433 ∙ NCBI:219854 ∙ OMIM:619285 ∙ HGNC:27344 ∙ Uniprot:A2RU14 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Joubert syndrome 39 (Strong), mode of inheritance: AR
• ciliopathy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 39	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic; Ophthalmologic	33791682

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM218 gene.

• not_specified (15 variants)
• Joubert_syndrome_39 (4 variants)
• Joubert_syndrome (3 variants)
• Meckel_syndrome,_type_4 (2 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM218 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001258244.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense	1	2	14	1		18
nonsense	1					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	2	2	15	1	0

Highest pathogenic variant AF is 0.0001332768

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM218	protein_coding	protein_coding	ENST00000455225	3	15262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00168	0.480	125733	0	12	125745	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.744	47	63.7	0.738	0.00000378	710
Missense in Polyphen		18	23.152	0.77746		248
Synonymous	-0.145	32	31.0	1.03	0.00000192	268
Loss of Function	0.0276	4	4.06	0.985	2.57e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000215	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in ciliary biogenesis or function. {ECO:0000250|UniProtKB:Q9CQ44}.

Intolerance Scores

• loftool: 0.485
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.198
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem218
• Phenotype: renal/urinary system phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Cellular component: cilium;integral component of membrane
• Molecular function: protein binding