TMEM202

transmembrane protein 202

Basic information

Region (hg38): 15:72398302-72408367

Links

ENSG00000187806 ∙ NCBI:338949 ∙ ∙ HGNC:33733 ∙ Uniprot:A6NGA9 ∙ 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 TMEM202 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM202 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in TMEM202

This is a list of pathogenic ClinVar variants found in the TMEM202 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-72398343-A-C		not specified	Uncertain significance (Dec 09, 2023)
15-72398376-C-A		not specified	Uncertain significance (Sep 22, 2022)
15-72398376-C-T		not specified	Uncertain significance (Dec 28, 2023)
15-72398378-A-C		not specified	Uncertain significance (Oct 26, 2021)
15-72398659-G-A		not specified	Uncertain significance (Jan 24, 2024)
15-72398741-G-A		not specified	Uncertain significance (Aug 04, 2023)
15-72398744-C-T		not specified	Likely benign (May 26, 2022)
15-72398781-G-A		not specified	Uncertain significance (Jul 05, 2022)
15-72398791-A-G		not specified	Uncertain significance (Sep 28, 2022)
15-72398795-C-G		not specified	Uncertain significance (Jun 13, 2024)
15-72398896-C-T		not specified	Uncertain significance (Aug 23, 2021)
15-72406632-T-G		not specified	Uncertain significance (Mar 19, 2024)
15-72406686-T-A		not specified	Uncertain significance (Sep 27, 2021)
15-72406740-G-A		not specified	Uncertain significance (Mar 04, 2024)
15-72407106-C-T		not specified	Uncertain significance (Mar 21, 2024)
15-72407121-G-A		not specified	Uncertain significance (May 29, 2024)
15-72407142-A-T		not specified	Uncertain significance (Sep 01, 2021)
15-72407172-A-G		not specified	Likely benign (Jun 19, 2024)
15-72407175-T-C		not specified	Uncertain significance (Dec 20, 2023)
15-72407210-G-A		not specified	Uncertain significance (Oct 18, 2021)
15-72407711-T-A		not specified	Uncertain significance (May 27, 2022)
15-72407724-G-T		not specified	Uncertain significance (Mar 25, 2024)
15-72407747-G-A		not specified	Uncertain significance (May 02, 2024)
15-72407790-C-T		not specified	Uncertain significance (Jan 24, 2024)
15-72407862-A-G		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM202	protein_coding	protein_coding	ENST00000341689	5	9757

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.98e-8	0.175	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.230	140	148	0.947	0.00000720	1778
Missense in Polyphen		37	38.562	0.9595		516
Synonymous	0.657	50	56.3	0.889	0.00000298	523
Loss of Function	0.204	12	12.8	0.938	7.74e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000434	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.843
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00534

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem202

Gene ontology

• Cellular component: plasma membrane;integral component of membrane