TMEM97

transmembrane protein 97

Basic information

Region (hg38): 17:28319200-28328685

Links

ENSG00000109084 ∙ NCBI:27346 ∙ OMIM:612912 ∙ HGNC:28106 ∙ Uniprot:Q5BJF2 ∙ 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 TMEM97 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM97 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in TMEM97

This is a list of pathogenic ClinVar variants found in the TMEM97 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28319346-G-T		not specified	Uncertain significance (Oct 24, 2023)
17-28325523-G-C		not specified	Uncertain significance (Jan 26, 2023)
17-28325555-A-G		not specified	Uncertain significance (Jun 06, 2023)
17-28326626-G-A		not specified	Uncertain significance (Mar 31, 2023)
17-28326673-G-C		not specified	Likely benign (Jan 16, 2024)
17-28326681-G-A		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM97	protein_coding	protein_coding	ENST00000226230	3	9587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000313	0.597	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.170	89	93.6	0.951	0.00000467	1131
Missense in Polyphen		34	40.038	0.8492		439
Synonymous	0.289	37	39.3	0.941	0.00000196	353
Loss of Function	0.599	6	7.81	0.769	3.98e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000567	0.000543
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000579	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.0000579	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intracellular orphan receptor that binds numerous drugs and which is highly expressed in various proliferating cancer cells (PubMed:28559337). Corresponds to the sigma-2 receptor, which is thought to play important role in regulating cell survival, morphology and differentiation (PubMed:23922215, PubMed:25620095). Under investigation for its potential diagnostic and therapeutic uses (PubMed:23922215, PubMed:25620095). May play a role as a regulator of cellular cholesterol homeostasis (PubMed:19583955). May function as sterol isomerase (PubMed:25566323). May alter the activity of some cytochrome P450 proteins (PubMed:22292588). {ECO:0000269|PubMed:19583955, ECO:0000269|PubMed:28559337, ECO:0000303|PubMed:22292588, ECO:0000303|PubMed:23922215, ECO:0000303|PubMed:25620095, ECO:0000305|PubMed:25566323}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.403
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0882
• hipred: N
• hipred_score: 0.325
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.255

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem97

Gene ontology

• Biological process: regulation of cell growth;cholesterol homeostasis
• Cellular component: lysosome;rough endoplasmic reticulum;cytosol;plasma membrane;integral component of membrane;rough endoplasmic reticulum membrane;nuclear membrane
• Molecular function: protein binding