TMEM204

transmembrane protein 204

Basic information

Region (hg38): 16:1528688-1555580

Previous symbols: [ "C16orf30" ]

Links

ENSG00000131634 ∙ NCBI:79652 ∙ OMIM:611002 ∙ HGNC:14158 ∙ Uniprot:Q9BSN7 ∙ 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 TMEM204 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM204 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		1
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	3	0

Variants in TMEM204

This is a list of pathogenic ClinVar variants found in the TMEM204 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1534282-G-A		not specified	Uncertain significance (Mar 25, 2024)
16-1534441-C-T		not specified	Uncertain significance (Jun 22, 2021)
16-1534448-G-T		not specified	Uncertain significance (May 20, 2024)
16-1534451-C-T		not specified	Likely benign (Oct 20, 2023)
16-1534483-G-A		not specified	Likely benign (Jan 23, 2023)
16-1534499-C-T		not specified	Uncertain significance (Sep 01, 2021)
16-1534514-C-G		not specified	Uncertain significance (Mar 06, 2023)
16-1534516-G-A		not specified	Uncertain significance (Oct 22, 2021)
16-1534547-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-1534549-G-A		not specified	Uncertain significance (May 13, 2024)
16-1541965-G-A		not specified	Uncertain significance (Apr 27, 2023)
16-1542019-C-G		not specified	Uncertain significance (Jan 03, 2024)
16-1542031-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-1542036-G-A			Likely benign (Dec 01, 2021)
16-1554818-G-A		not specified	Uncertain significance (Nov 18, 2022)
16-1554844-T-C		not specified	Uncertain significance (Jan 31, 2023)
16-1554884-C-T		Saldino-Mainzer syndrome	Uncertain significance (Sep 25, 2018)
16-1554930-G-T		not specified	Uncertain significance (May 13, 2024)
16-1554965-G-A		not specified	Uncertain significance (Apr 13, 2022)
16-1554992-G-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM204	protein_coding	protein_coding	ENST00000566264	3	26893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.913	0.0867	124758	0	5	124763	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.994	124	159	0.778	0.0000112	1423
Missense in Polyphen		58	95.94	0.60455		832
Synonymous	-0.282	79	75.9	1.04	0.00000571	506
Loss of Function	2.60	0	7.84	0.00	4.35e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000112	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can influence paracellular permeability. Appears to be involved in cell-cell interactions through adherens.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.0765
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.406
• hipred: Y
• hipred_score: 0.654
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem204
• Phenotype: muscle phenotype; immune system phenotype

Gene ontology

• Biological process: lymph vessel development;regulation of vascular endothelial growth factor receptor signaling pathway;smooth muscle cell differentiation
• Cellular component: plasma membrane;adherens junction;integral component of membrane