TMEM104

transmembrane protein 104

Basic information

Region (hg38): 17:74776499-74839753

Links

ENSG00000109066 ∙ NCBI:54868 ∙ ∙ HGNC:25984 ∙ Uniprot:Q8NE00 ∙ 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 TMEM104 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM104 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			37	2	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	2	2

Variants in TMEM104

This is a list of pathogenic ClinVar variants found in the TMEM104 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74777346-A-G		not specified	Uncertain significance (Nov 08, 2022)
17-74777355-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-74785554-G-A		not specified	Uncertain significance (Sep 06, 2022)
17-74785563-C-G		not specified	Uncertain significance (Jun 23, 2023)
17-74785575-G-A		not specified	Uncertain significance (Aug 13, 2021)
17-74785599-A-C		not specified	Uncertain significance (Jun 29, 2023)
17-74790215-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-74790238-C-T			Benign (Sep 28, 2017)
17-74790252-G-A		not specified	Likely benign (Oct 04, 2022)
17-74790266-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-74790975-C-G		not specified	Uncertain significance (Sep 07, 2022)
17-74790994-C-T		not specified	Uncertain significance (Mar 07, 2024)
17-74790995-G-A		not specified	Uncertain significance (Dec 02, 2022)
17-74791005-G-A		not specified	Uncertain significance (Aug 15, 2023)
17-74791035-A-C		not specified	Uncertain significance (Jun 02, 2023)
17-74795018-T-C		not specified	Uncertain significance (May 06, 2024)
17-74795065-G-A		not specified	Uncertain significance (Feb 27, 2024)
17-74795080-G-A		not specified	Uncertain significance (Nov 22, 2022)
17-74795534-G-C		not specified	Uncertain significance (Feb 13, 2024)
17-74795549-G-A		not specified	Uncertain significance (Aug 17, 2021)
17-74795562-A-T		not specified	Uncertain significance (Mar 01, 2024)
17-74795565-C-T		not specified	Uncertain significance (May 08, 2023)
17-74795585-C-T		not specified	Uncertain significance (May 25, 2022)
17-74795600-C-G			Benign (Sep 28, 2017)
17-74795622-G-A		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM104	protein_coding	protein_coding	ENST00000335464	9	63297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000382	0.990	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	319	337	0.946	0.0000232	3225
Missense in Polyphen		78	106.72	0.73088		1105
Synonymous	-2.01	180	149	1.21	0.0000114	1023
Loss of Function	2.30	11	22.9	0.481	0.00000135	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.613
• rvis_EVS: 0.14
• rvis_percentile_EVS: 63.62

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.394
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem104

Gene ontology

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