TMEM88

transmembrane protein 88

Basic information

Region (hg38): 17:7855066-7856099

Links

ENSG00000167874 ∙ NCBI:92162 ∙ OMIM:617813 ∙ HGNC:32371 ∙ Uniprot:Q6PEY1 ∙ 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 TMEM88 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM88 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in TMEM88

This is a list of pathogenic ClinVar variants found in the TMEM88 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7855081-G-A		not specified	Uncertain significance (Apr 24, 2024)
17-7855088-C-G		not specified	Uncertain significance (Dec 26, 2023)
17-7855100-G-A		not specified	Uncertain significance (Sep 14, 2023)
17-7855108-C-T		not specified	Uncertain significance (Mar 11, 2022)
17-7855147-T-G		not specified	Uncertain significance (Dec 14, 2022)
17-7855165-G-C		not specified	Uncertain significance (May 05, 2023)
17-7855165-G-T		not specified	Uncertain significance (Feb 06, 2024)
17-7855451-C-G		not specified	Uncertain significance (Jun 17, 2022)
17-7855484-C-G		not specified	Uncertain significance (Jul 12, 2022)
17-7855485-G-A		not specified	Uncertain significance (Jun 07, 2024)
17-7855550-G-A		not specified	Uncertain significance (Jun 10, 2024)
17-7855566-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-7855617-G-A		not specified	Uncertain significance (May 03, 2023)
17-7855622-C-G		not specified	Uncertain significance (Feb 21, 2024)
17-7855628-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-7855637-C-A		not specified	Uncertain significance (Nov 06, 2023)
17-7855685-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-7855688-C-G		not specified	Uncertain significance (Oct 12, 2021)
17-7855698-G-T		not specified	Uncertain significance (Oct 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM88	protein_coding	protein_coding	ENST00000301599	2	1035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.277	0.640	125361	0	18	125379	0.0000718

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.337	94	104	0.907	0.00000641	946
Missense in Polyphen		35	45.021	0.77742		415
Synonymous	-0.722	54	47.7	1.13	0.00000283	391
Loss of Function	1.31	1	3.72	0.269	2.03e-7	31

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000909
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.0000621	0.0000466
European (Non-Finnish)	0.0000834	0.0000794
Middle Eastern	0.0000549	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the Wnt/beta-catenin signaling pathway. Crucial for heart development and acts downstream of GATA factors in the pre-cardiac mesoderm to specify lineage commitment of cardiomyocyte development. {ECO:0000269|PubMed:23924634}.

Intolerance Scores

• loftool: 0.423
• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.96

Haploinsufficiency Scores

• pHI: 0.383
• hipred: N
• hipred_score: 0.208

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.326

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem88

Zebrafish Information Network

• Gene name: tmem88a
• Affected structure: myeloid cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: multicellular organism development;Wnt signaling pathway;protein stabilization;protein localization to plasma membrane;negative regulation of canonical Wnt signaling pathway
• Cellular component: cytosol;plasma membrane;integral component of membrane
• Molecular function: protein binding;PDZ domain binding