TMEM223

transmembrane protein 223

Basic information

Region (hg38): 11:62771628-62792006

Links

ENSG00000168569 ∙ NCBI:79064 ∙ ∙ HGNC:28464 ∙ Uniprot:A0PJW6 ∙ 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 TMEM223 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM223 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11			11
Total	0	0	33	0	0

Variants in TMEM223

This is a list of pathogenic ClinVar variants found in the TMEM223 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62775884-C-T		not specified	Uncertain significance (Oct 02, 2023)
11-62778000-A-T		not specified	Uncertain significance (Sep 30, 2022)
11-62778032-G-A		not specified	Uncertain significance (Oct 27, 2021)
11-62778053-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-62778922-G-A		not specified	Uncertain significance (Feb 13, 2023)
11-62781928-T-C		not specified	Uncertain significance (Aug 10, 2021)
11-62781934-C-T		not specified	Uncertain significance (May 04, 2022)
11-62781939-C-G		not specified	Uncertain significance (Jun 22, 2023)
11-62782180-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-62782183-A-C		not specified	Uncertain significance (Apr 01, 2024)
11-62782213-G-A		not specified	Uncertain significance (Nov 14, 2023)
11-62782270-A-G		not specified	Uncertain significance (Jan 04, 2024)
11-62782321-G-A		not specified	Uncertain significance (May 09, 2023)
11-62782713-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-62782724-C-A		not specified	Uncertain significance (Jan 04, 2022)
11-62782796-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-62786623-G-A		not specified	Uncertain significance (May 09, 2023)
11-62786623-G-C		not specified	Uncertain significance (Oct 06, 2022)
11-62786653-G-A		not specified	Uncertain significance (Nov 12, 2021)
11-62786722-C-T		not specified	Uncertain significance (Jun 02, 2024)
11-62786811-G-T		not specified	Uncertain significance (Dec 01, 2022)
11-62786829-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-62786875-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-62786922-G-A		not specified	Uncertain significance (Jan 02, 2024)
11-62786922-G-C		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM223	protein_coding	protein_coding	ENST00000307366	2	20393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000150	0.249	124305	0	45	124350	0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.468	129	115	1.12	0.00000603	1221
Missense in Polyphen		36	39.951	0.9011		415
Synonymous	-0.676	54	48.0	1.12	0.00000221	466
Loss of Function	-0.203	7	6.44	1.09	4.27e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000300	0.000278
Finnish	0.000148	0.000139
European (Non-Finnish)	0.000134	0.000124
Middle Eastern	0.000300	0.000278
South Asian	0.000211	0.000164
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.783
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.16

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: nervous system development
• Cellular component: integral component of membrane