TMEM200A

transmembrane protein 200A

Basic information

Region (hg38): 6:130366017-130443067

Previous symbols: [ "KIAA1913" ]

Links

ENSG00000164484 ∙ NCBI:114801 ∙ ∙ HGNC:21075 ∙ Uniprot:Q86VY9 ∙ 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 TMEM200A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM200A 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in TMEM200A

This is a list of pathogenic ClinVar variants found in the TMEM200A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-130440477-T-C		not specified	Uncertain significance (May 17, 2023)
6-130440594-T-C		not specified	Uncertain significance (Feb 12, 2024)
6-130440614-T-A		not specified	Uncertain significance (Jul 09, 2021)
6-130440950-G-C		not specified	Uncertain significance (Sep 14, 2023)
6-130440993-G-A		not specified	Uncertain significance (Nov 19, 2022)
6-130441048-C-G		not specified	Uncertain significance (Apr 25, 2022)
6-130441051-T-C		not specified	Uncertain significance (Jun 07, 2024)
6-130441084-G-T		not specified	Uncertain significance (Dec 19, 2023)
6-130441113-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-130441137-T-A		not specified	Uncertain significance (Aug 09, 2021)
6-130441143-C-T		not specified	Uncertain significance (May 27, 2022)
6-130441152-C-T		not specified	Uncertain significance (Jun 07, 2023)
6-130441233-G-A		not specified	Uncertain significance (Jan 19, 2024)
6-130441237-C-G		not specified	Uncertain significance (Jun 23, 2023)
6-130441336-T-C		not specified	Uncertain significance (Mar 24, 2023)
6-130441347-A-G		not specified	Uncertain significance (May 11, 2022)
6-130441377-T-A		not specified	Uncertain significance (Dec 15, 2021)
6-130441402-T-C		not specified	Uncertain significance (Jan 20, 2023)
6-130441443-G-A		not specified	Uncertain significance (Dec 06, 2021)
6-130441496-G-T		not specified	Uncertain significance (Mar 28, 2022)
6-130441549-G-C		not specified	Uncertain significance (Sep 01, 2021)
6-130441573-C-A		not specified	Uncertain significance (Apr 08, 2022)
6-130441627-G-A		not specified	Uncertain significance (Jan 19, 2024)
6-130441771-T-A		not specified	Uncertain significance (Apr 21, 2022)
6-130441789-A-G		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM200A	protein_coding	protein_coding	ENST00000392429	1	77330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.851	0.149	125657	0	7	125664	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.662	254	285	0.890	0.0000159	3242
Missense in Polyphen		78	108.33	0.72		1222
Synonymous	0.147	105	107	0.982	0.00000603	984
Loss of Function	2.74	1	10.6	0.0942	5.12e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000440
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.0411
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.737
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem200a

Gene ontology

• Cellular component: integral component of membrane