TMEM143

transmembrane protein 143

Basic information

Region (hg38): 19:48332355-48364059

Links

ENSG00000161558 ∙ NCBI:55260 ∙ ∙ HGNC:25603 ∙ Uniprot:Q96AN5 ∙ 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 TMEM143 gene.

• Inborn genetic diseases (36 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM143 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			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	0

Variants in TMEM143

This is a list of pathogenic ClinVar variants found in the TMEM143 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48333262-G-T		not specified	Uncertain significance (Aug 16, 2022)
19-48333295-C-G		not specified	Uncertain significance (Dec 03, 2021)
19-48333305-G-C		not specified	Uncertain significance (Feb 15, 2023)
19-48333373-T-G		not specified	Uncertain significance (Jun 24, 2022)
19-48333399-G-T		not specified	Uncertain significance (Mar 23, 2023)
19-48334028-C-A		not specified	Uncertain significance (Sep 28, 2022)
19-48334055-T-C		not specified	Uncertain significance (Jan 29, 2024)
19-48334097-A-C		not specified	Uncertain significance (Dec 01, 2022)
19-48334124-T-C		not specified	Uncertain significance (Dec 17, 2023)
19-48334133-G-C		not specified	Uncertain significance (Feb 24, 2022)
19-48334133-G-T		not specified	Uncertain significance (Feb 23, 2023)
19-48334172-T-C		not specified	Uncertain significance (May 05, 2023)
19-48334176-C-A		not specified	Uncertain significance (Feb 23, 2023)
19-48342559-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-48342567-A-C		not specified	Uncertain significance (Feb 13, 2024)
19-48342598-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-48342621-T-C		not specified	Uncertain significance (Jan 26, 2023)
19-48342625-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-48342690-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-48342696-T-G		not specified	Uncertain significance (Sep 21, 2023)
19-48342732-G-A		not specified	Uncertain significance (Mar 02, 2023)
19-48342765-C-G		not specified	Uncertain significance (Aug 04, 2023)
19-48342769-G-A		not specified	Uncertain significance (Sep 13, 2023)
19-48342780-G-A		not specified	Uncertain significance (Dec 20, 2021)
19-48343349-A-G		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM143	protein_coding	protein_coding	ENST00000293261	8	31882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.79e-12	0.0481	125168	9	570	125747	0.00230

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.205	268	278	0.965	0.0000160	2885
Missense in Polyphen		83	95.931	0.86521		987
Synonymous	-0.384	137	131	1.04	0.00000787	1020
Loss of Function	0.154	18	18.7	0.962	8.88e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00118
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0203	0.0201
Finnish	0.00156	0.00148
European (Non-Finnish)	0.000795	0.000774
Middle Eastern	0.0203	0.0201
South Asian	0.00106	0.00105
Other	0.00348	0.00326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0745

Intolerance Scores

• loftool: 0.766
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.170
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem143

Gene ontology

• Biological process: biological_process
• Cellular component: mitochondrion;integral component of membrane
• Molecular function: molecular_function