TMEM54

transmembrane protein 54

Basic information

Region (hg38): 1:32894594-32901438

Links

ENSG00000121900 ∙ NCBI:113452 ∙ ∙ HGNC:24143 ∙ Uniprot:Q969K7 ∙ 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 TMEM54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM54 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			15			15
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in TMEM54

This is a list of pathogenic ClinVar variants found in the TMEM54 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32894824-GAGCTGGTGCAGCTC-G		not specified	Likely benign (Dec 21, 2023)
1-32894849-G-C		not specified	Uncertain significance (Feb 07, 2023)
1-32894861-G-C		not specified	Uncertain significance (Feb 27, 2023)
1-32895327-C-G		not specified	Uncertain significance (Sep 29, 2022)
1-32895354-T-C		not specified	Uncertain significance (Dec 06, 2022)
1-32895372-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-32895373-G-T		not specified	Uncertain significance (Mar 15, 2024)
1-32895397-C-A		not specified	Uncertain significance (Dec 17, 2023)
1-32895397-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-32895412-C-T		not specified	Uncertain significance (Dec 30, 2023)
1-32895676-A-G		not specified	Uncertain significance (Jun 03, 2022)
1-32895734-C-G		not specified	Uncertain significance (Jun 10, 2024)
1-32895962-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-32898128-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-32898161-C-T		not specified	Uncertain significance (Mar 15, 2024)
1-32898200-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-32898230-C-A		not specified	Uncertain significance (Oct 26, 2022)
1-32898274-C-A		not specified	Uncertain significance (Dec 03, 2021)
1-32898302-C-A		not specified	Uncertain significance (Aug 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM54	protein_coding	protein_coding	ENST00000373463	6	6845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00309	0.831	125686	1	43	125730	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.743	115	140	0.823	0.00000883	1389
Missense in Polyphen		45	56.548	0.79578		549
Synonymous	0.424	55	59.2	0.930	0.00000374	491
Loss of Function	1.15	5	8.64	0.579	3.67e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000280	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.000280	0.000272
South Asian	0.000737	0.000686
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.696
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.256
• hipred: N
• hipred_score: 0.146
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.212

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem54

Gene ontology

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