TMEM201

transmembrane protein 201

Basic information

Region (hg38): 1:9588911-9614877

Links

ENSG00000188807 ∙ NCBI:199953 ∙ ∙ HGNC:33719 ∙ Uniprot:Q5SNT2 ∙ 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 TMEM201 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM201 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				1	4	5
missense			46	2	3	51
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	47	3	7

Variants in TMEM201

This is a list of pathogenic ClinVar variants found in the TMEM201 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-9588972-C-G			Likely benign (May 01, 2022)
1-9588995-T-C		not specified	Uncertain significance (Apr 04, 2024)
1-9595907-C-T			Benign (Mar 29, 2018)
1-9595931-A-G		not specified	Uncertain significance (Sep 29, 2023)
1-9595939-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-9595961-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-9596865-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-9596879-G-A			Benign (Apr 04, 2018)
1-9596940-G-A		not specified	Uncertain significance (Feb 02, 2024)
1-9597033-G-A		not specified	Uncertain significance (Nov 13, 2023)
1-9597045-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-9597060-C-T			Benign (Nov 11, 2017)
1-9598454-G-T		not specified	Uncertain significance (Apr 13, 2023)
1-9598512-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-9598513-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-9598619-C-T			Benign (Jun 29, 2018)
1-9601131-G-A			Benign (Apr 04, 2018)
1-9601162-T-C		not specified	Uncertain significance (May 30, 2023)
1-9601192-G-A		not specified	Likely benign (Oct 26, 2022)
1-9601193-C-T		not specified	Uncertain significance (May 15, 2024)
1-9601214-A-G		not specified	Uncertain significance (Dec 13, 2023)
1-9601226-G-T		not specified	Uncertain significance (Sep 29, 2023)
1-9601292-C-T		not specified	Uncertain significance (Sep 27, 2022)
1-9601293-C-A			Benign (Mar 29, 2018)
1-9601368-G-C		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM201	protein_coding	protein_coding	ENST00000340381	11	26004

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00996	125507	0	6	125513	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	350	427	0.819	0.0000296	4211
Missense in Polyphen		145	180.68	0.80254		1818
Synonymous	0.315	197	203	0.972	0.0000148	1483
Loss of Function	4.29	3	27.1	0.111	0.00000144	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.00000935	0.00000882
Middle Eastern	0.000163	0.000163
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in nuclear movement during fibroblast polarization and migration. Proposed to be involved in actin- dependent nuclear movement via association with transmembrane actin-associated nuclear (TAN) lines which are bound to F-actin cables and couple the nucleus to retrograde actin flow (By similarity). Overexpression can recruit Ran GTPase to the nuclear periphery (PubMed:27541860). {ECO:0000250|UniProtKB:A2A8U2, ECO:0000305|PubMed:27541860}.

Intolerance Scores

• loftool: 0.0119
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• pHI: 0.305
• hipred: Y
• hipred_score: 0.570
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.473

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem201

Gene ontology

• Biological process: fibroblast migration;nuclear migration along microtubule
• Cellular component: spindle pole;integral component of nuclear inner membrane;cytoplasm;nuclear membrane
• Molecular function: lamin binding;actin filament binding