TMEM190

transmembrane protein 190

Basic information

Region (hg38): 19:55376826-55378246

Links

ENSG00000160472 ∙ NCBI:147744 ∙ ∙ HGNC:29632 ∙ Uniprot:Q8WZ59 ∙ 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 TMEM190 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM190 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	3		19
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	3	0

Variants in TMEM190

This is a list of pathogenic ClinVar variants found in the TMEM190 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55376894-T-A		not specified	Uncertain significance (Mar 25, 2024)
19-55377620-A-T		not specified	Uncertain significance (Jan 23, 2024)
19-55377629-G-C		not specified	Uncertain significance (Jun 17, 2024)
19-55377643-A-G		not specified	Uncertain significance (Dec 08, 2021)
19-55377650-G-T		not specified	Uncertain significance (Oct 27, 2022)
19-55377692-G-A		not specified	Uncertain significance (May 23, 2023)
19-55377710-G-A		not specified	Uncertain significance (Jun 29, 2023)
19-55377841-C-T		not specified	Uncertain significance (May 31, 2024)
19-55377985-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-55377986-G-A		not specified	Uncertain significance (Aug 16, 2022)
19-55377994-G-A		not specified	Likely benign (Aug 13, 2021)
19-55377994-G-C		not specified	Likely benign (Jun 24, 2022)
19-55378001-A-G		not specified	Uncertain significance (Apr 25, 2023)
19-55378025-C-T		not specified	Uncertain significance (Mar 05, 2024)
19-55378040-A-G		not specified	Likely benign (Dec 08, 2023)
19-55378045-G-A		not specified	Uncertain significance (May 17, 2023)
19-55378073-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-55378082-C-T		not specified	Uncertain significance (Mar 20, 2024)
19-55378091-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-55378099-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-55378147-G-A		not specified	Uncertain significance (Nov 03, 2023)
19-55378160-C-G		not specified	Uncertain significance (Jan 02, 2024)
19-55378169-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-55378186-G-A		not specified	Uncertain significance (Mar 29, 2024)
19-55378196-A-T		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM190	protein_coding	protein_coding	ENST00000291934	5	1409

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00126	0.659	125532	0	6	125538	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.206	105	111	0.945	0.00000613	1136
Missense in Polyphen		20	18.955	1.0551		196
Synonymous	-0.834	55	47.7	1.15	0.00000267	357
Loss of Function	0.660	5	6.87	0.728	2.93e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000889	0.00000881
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.142
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.220
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem190
• Phenotype: normal phenotype

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation
• Cellular component: inner acrosomal membrane;nucleus;integral component of membrane
• Molecular function: protein binding;protein self-association