TMEM204

protein-coding

transmembrane protein 204

Gene summary

C16ORF30 plays a role in cell adhesion and cellular permeability at adherens junctions (Kearsey et al., 2004 [PubMed 15206924]).[supplied by OMIM, Mar 2008]

Previous symbols:

C16orf30

MANE transcript

NM_024600.6

Inheritance

—

ClinVar variants

U:37B:7

Top phenotype

Saldino-Mainzer syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr16:1,528,688-1,555,580

External References & Databases

Ensembl (ENSG00000131634)

Transcript & Mutation Effects

hg38 • Region Span ~26.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM204 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 5

Saldino-Mainzer syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024600.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			37 clinvar	3 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	7	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024600.6	RefSeq	NP_078876.2	3	MANE Select
ENST00000566264.2	Ensembl	ENSP00000454945.1	3	MANE Select
NM_001256541.2	RefSeq	NP_001243470.1	3	Standard
ENST00000253934.10	Ensembl	ENSP00000253934.5	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000566264
Coding exons: 3
Length: 26893
Individuals with no LoFs: 124758
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 124763
p: 0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.994	124	159	0.778	0.0000112	1423
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.162

Gene Damage Prediction

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