TMEM102

transmembrane protein 102

Basic information

Region (hg38): 17:7435434-7437679

Links

ENSG00000181284 ∙ NCBI:284114 ∙ OMIM:613936 ∙ HGNC:26722 ∙ Uniprot:Q8N9M5 ∙ 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 TMEM102 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM102 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in TMEM102

This is a list of pathogenic ClinVar variants found in the TMEM102 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7435909-G-T		not specified	Uncertain significance (May 31, 2023)
17-7435912-C-A		not specified	Uncertain significance (May 23, 2024)
17-7435945-A-T		not specified	Uncertain significance (Jul 12, 2022)
17-7436020-G-T		not specified	Uncertain significance (Apr 08, 2022)
17-7436034-A-C		not specified	Uncertain significance (May 30, 2024)
17-7436056-G-A		not specified	Likely benign (Jan 27, 2022)
17-7436214-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-7436287-A-G		not specified	Uncertain significance (Apr 20, 2024)
17-7436406-C-G		not specified	Uncertain significance (May 15, 2024)
17-7436425-T-C		not specified	Uncertain significance (Nov 30, 2021)
17-7436615-C-G		not specified	Uncertain significance (Jul 14, 2023)
17-7436785-G-T		not specified	Uncertain significance (Dec 13, 2023)
17-7436842-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-7436859-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-7436896-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-7436925-T-C		not specified	Uncertain significance (Jan 07, 2022)
17-7436991-G-A		not specified	Uncertain significance (May 08, 2024)
17-7437139-C-G		not specified	Uncertain significance (Apr 07, 2022)
17-7437174-G-C		not specified	Uncertain significance (May 14, 2024)
17-7437219-T-C		not specified	Uncertain significance (Mar 20, 2024)
17-7437258-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-7437268-C-G		not specified	Uncertain significance (Feb 22, 2023)
17-7437279-T-C		not specified	Uncertain significance (Jun 28, 2023)
17-7437285-G-A		not specified	Uncertain significance (Jun 01, 2023)
17-7437286-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM102	protein_coding	protein_coding	ENST00000323206	2	2237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000857	0.777	124115	5	1621	125741	0.00649

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.921	228	271	0.842	0.0000130	3136
Missense in Polyphen		98	112	0.87504		1360
Synonymous	1.11	113	129	0.876	0.00000667	1190
Loss of Function	1.22	10	15.1	0.661	7.12e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00567	0.00561
Ashkenazi Jewish	0.00475	0.00437
East Asian	0.000220	0.000217
Finnish	0.00703	0.00695
European (Non-Finnish)	0.0106	0.0103
Middle Eastern	0.000220	0.000217
South Asian	0.00166	0.00160
Other	0.00771	0.00752

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Selectively involved in CSF2 deprivation-induced apoptosis via a mitochondria-dependent pathway. {ECO:0000269|PubMed:17828305}.

Recessive Scores

• pRec: 0.0992

Haploinsufficiency Scores

• pHI: 0.175
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem102

Gene ontology

• Biological process: apoptotic process;signal transduction;positive regulation of T cell chemotaxis;response to cytokine;positive regulation of cell adhesion;regulation of peptidyl-tyrosine phosphorylation;regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;positive regulation of T cell migration
• Cellular component: mitochondrion;plasma membrane;cell surface;integral component of membrane;protein-containing complex
• Molecular function: protein binding