TMEM154

transmembrane protein 154

Basic information

Region (hg38): 4:152618628-152680012

Links

ENSG00000170006 ∙ NCBI:201799 ∙ ∙ HGNC:26489 ∙ Uniprot:Q6P9G4 ∙ 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 TMEM154 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM154 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	9	2	0

Variants in TMEM154

This is a list of pathogenic ClinVar variants found in the TMEM154 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-152628565-T-TAAAAAAAAAAAAA			Likely benign (Sep 01, 2022)
4-152628565-T-TAAAAAAAAAAA			Likely benign (Nov 01, 2022)
4-152640967-G-A		not specified	Uncertain significance (Jan 19, 2024)
4-152643098-C-T		not specified	Uncertain significance (Feb 08, 2023)
4-152644416-C-G		not specified	Uncertain significance (Feb 14, 2023)
4-152644421-A-G		not specified	Uncertain significance (Feb 10, 2023)
4-152652696-G-A		not specified	Likely benign (Nov 18, 2022)
4-152652712-C-T		not specified	Uncertain significance (Nov 21, 2022)
4-152652754-C-A		not specified	Uncertain significance (Jul 06, 2021)
4-152652786-G-A		not specified	Uncertain significance (Sep 26, 2023)
4-152652814-C-T		not specified	Likely benign (Dec 15, 2023)
4-152679921-G-C		not specified	Uncertain significance (May 31, 2022)
4-152679927-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM154	protein_coding	protein_coding	ENST00000304385	7	61534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.87e-7	0.210	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.877	119	94.9	1.25	0.00000436	1197
Missense in Polyphen		21	17.192	1.2215		176
Synonymous	0.782	30	36.0	0.834	0.00000180	327
Loss of Function	0.0976	10	10.3	0.967	4.33e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000569	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000439
Middle Eastern	0.000569	0.000544
South Asian	0.0000391	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0393
• hipred: N
• hipred_score: 0.123
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem154

Gene ontology

• Cellular component: integral component of membrane