TMEM220

transmembrane protein 220

Basic information

Region (hg38): 17:10699015-10730023

Links

ENSG00000187824 ∙ NCBI:388335 ∙ ∙ HGNC:33757 ∙ Uniprot:Q6QAJ8 ∙ 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 TMEM220 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM220 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			10	2	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	1

Variants in TMEM220

This is a list of pathogenic ClinVar variants found in the TMEM220 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-10704939-C-T		not specified	Uncertain significance (Apr 06, 2023)
17-10704972-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-10705031-T-A		not specified	Uncertain significance (Mar 18, 2024)
17-10705050-C-T		not specified	Uncertain significance (Jun 04, 2024)
17-10705079-C-A		not specified	Uncertain significance (Jan 31, 2024)
17-10705143-G-A		not specified	Uncertain significance (Jun 22, 2023)
17-10705166-T-A		not specified	Uncertain significance (Dec 11, 2023)
17-10705182-T-C		not specified	Uncertain significance (Jan 04, 2022)
17-10710857-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-10710861-C-G		not specified	Uncertain significance (Nov 27, 2023)
17-10710917-C-G		not specified	Uncertain significance (Apr 12, 2023)
17-10710938-T-A		not specified	Uncertain significance (Dec 19, 2023)
17-10710971-G-A		not specified	Uncertain significance (Jan 09, 2024)
17-10711086-G-A		not specified	Uncertain significance (Apr 13, 2022)
17-10711089-G-A		not specified	Uncertain significance (Apr 04, 2023)
17-10715491-G-A		not specified	Uncertain significance (Nov 19, 2022)
17-10715538-A-G		not specified	Uncertain significance (May 30, 2023)
17-10715563-A-G			Likely benign (Mar 01, 2022)
17-10723277-A-C		not specified	Uncertain significance (Apr 04, 2023)
17-10723318-C-T		not specified	Uncertain significance (Apr 09, 2024)
17-10725047-C-T			Benign (Mar 29, 2018)
17-10725086-G-A		not specified	Likely benign (Apr 12, 2022)
17-10725105-T-C			Likely benign (Mar 01, 2022)
17-10725130-A-T		not specified	Uncertain significance (Sep 29, 2023)
17-10726255-T-C		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM220	protein_coding	protein_coding	ENST00000341871	6	31302

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000130	0.222	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	65	81.2	0.801	0.00000388	1012
Missense in Polyphen		23	27.324	0.84175		384
Synonymous	-0.513	33	29.5	1.12	0.00000146	311
Loss of Function	0.0100	9	9.03	0.996	3.84e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000844	0.000828
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.509
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem220

Gene ontology

• Cellular component: integral component of membrane