TMEM209

transmembrane protein 209

Basic information

Region (hg38): 7:130164713-130207770

Links

ENSG00000146842 ∙ NCBI:84928 ∙ ∙ HGNC:21898 ∙ Uniprot:Q96SK2 ∙ 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 TMEM209 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM209 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in TMEM209

This is a list of pathogenic ClinVar variants found in the TMEM209 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130170412-G-A		not specified	Uncertain significance (Apr 13, 2023)
7-130173837-G-T		not specified	Uncertain significance (May 16, 2024)
7-130175576-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-130178452-T-G		not specified	Uncertain significance (Mar 28, 2024)
7-130181652-C-T		not specified	Uncertain significance (Nov 07, 2022)
7-130181717-C-A		not specified	Uncertain significance (Jan 03, 2024)
7-130185200-C-A		not specified	Uncertain significance (Nov 13, 2023)
7-130185353-T-C		not specified	Uncertain significance (Mar 19, 2024)
7-130192632-C-G		not specified	Uncertain significance (May 04, 2023)
7-130192667-T-C		not specified	Uncertain significance (Mar 07, 2023)
7-130192717-T-C		not specified	Uncertain significance (Oct 12, 2021)
7-130192739-G-A		not specified	Uncertain significance (Jun 10, 2022)
7-130192739-G-T		not specified	Uncertain significance (Oct 02, 2023)
7-130192762-C-A		not specified	Uncertain significance (May 04, 2023)
7-130192792-G-A		not specified	Uncertain significance (Dec 20, 2023)
7-130192819-G-A		not specified	Uncertain significance (Jul 30, 2023)
7-130201867-C-T		not specified	Likely benign (Nov 08, 2022)
7-130201872-G-A		not specified	Uncertain significance (Oct 05, 2021)
7-130202002-T-G		not specified	Uncertain significance (Dec 20, 2023)
7-130202073-G-T		not specified	Uncertain significance (Aug 08, 2022)
7-130202085-T-A		not specified	Uncertain significance (Dec 28, 2022)
7-130202648-G-C		not specified	Uncertain significance (Jan 10, 2022)
7-130203985-T-C		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM209	protein_coding	protein_coding	ENST00000397622	15	43056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.05e-13	0.590	123066	11	1578	124655	0.00639

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.746	268	305	0.880	0.0000156	3659
Missense in Polyphen		62	96.42	0.64302		1236
Synonymous	0.530	103	110	0.936	0.00000633	1059
Loss of Function	1.53	24	33.6	0.715	0.00000178	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00403	0.00403
Ashkenazi Jewish	0.00203	0.00199
East Asian	0.000453	0.000445
Finnish	0.0114	0.0113
European (Non-Finnish)	0.00530	0.00525
Middle Eastern	0.000453	0.000445
South Asian	0.0199	0.0191
Other	0.00688	0.00679

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.798
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.426
• ghis: 0.618

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.765

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem209

Gene ontology

• Cellular component: integral component of membrane