TMEM89

transmembrane protein 89

Basic information

Region (hg38): 3:48620759-48621769

Links

ENSG00000183396 ∙ NCBI:440955 ∙ ∙ HGNC:32372 ∙ Uniprot:A2RUT3 ∙ 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 TMEM89 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM89 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in TMEM89

This is a list of pathogenic ClinVar variants found in the TMEM89 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48620846-C-T		not specified	Uncertain significance (Jan 06, 2023)
3-48620882-C-T		not specified	Likely benign (Jul 26, 2022)
3-48620946-G-C		not specified	Uncertain significance (Oct 02, 2023)
3-48620955-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-48620981-G-A		not specified	Uncertain significance (Jul 19, 2023)
3-48620984-C-T		not specified	Uncertain significance (May 22, 2023)
3-48620985-G-A		not specified	Uncertain significance (Jul 13, 2021)
3-48620987-C-A		not specified	Uncertain significance (Apr 12, 2023)
3-48620988-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-48621023-G-A		not specified	Uncertain significance (May 25, 2022)
3-48621479-T-C		not specified	Uncertain significance (Aug 08, 2023)
3-48621491-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-48621503-A-G		not specified	Uncertain significance (May 04, 2022)
3-48621525-T-C		not specified	Uncertain significance (Jan 30, 2024)
3-48621527-G-A		not specified	Uncertain significance (Jan 23, 2023)
3-48621549-C-A		not specified	Uncertain significance (Jun 18, 2021)
3-48621552-C-T		not specified	Uncertain significance (May 09, 2024)
3-48621608-C-A		not specified	Uncertain significance (Jan 03, 2024)
3-48621707-G-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM89	protein_coding	protein_coding	ENST00000330862	2	1097

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.770	0.223	125707	0	5	125712	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.124	111	107	1.03	0.00000712	991
Missense in Polyphen		31	25.589	1.2115		290
Synonymous	-0.561	51	46.1	1.11	0.00000281	368
Loss of Function	2.04	0	4.86	0.00	2.09e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.160
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.0679
• hipred: N
• hipred_score: 0.173

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem89

Gene ontology

• Cellular component: nucleus;integral component of membrane