TMEM9

transmembrane protein 9

Basic information

Region (hg38): 1:201134771-201171574

Links

ENSG00000116857 ∙ NCBI:252839 ∙ OMIM:616877 ∙ HGNC:18823 ∙ Uniprot:Q9P0T7 ∙ 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 TMEM9 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM9 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in TMEM9

This is a list of pathogenic ClinVar variants found in the TMEM9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201135719-G-C		not specified	Uncertain significance (Aug 03, 2022)
1-201135775-C-A		not specified	Uncertain significance (Jul 11, 2023)
1-201143836-T-C		not specified	Uncertain significance (May 11, 2022)
1-201146807-T-C		not specified	Uncertain significance (Dec 17, 2023)
1-201146816-A-G		not specified	Uncertain significance (Dec 27, 2023)
1-201151825-T-C		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM9	protein_coding	protein_coding	ENST00000367330	5	36803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00363	0.855	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	77	110	0.703	0.00000647	1184
Missense in Polyphen		29	49.019	0.59161		489
Synonymous	-0.223	46	44.1	1.04	0.00000250	368
Loss of Function	1.23	5	8.99	0.556	4.67e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in intracellular transport.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.402
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.568
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.515

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem9

Gene ontology

• Biological process: biological_process
• Cellular component: lysosome;lysosomal membrane;late endosome;integral component of membrane;late endosome membrane
• Molecular function: molecular_function