TMEM45A

transmembrane protein 45A

Basic information

Region (hg38): 3:100492619-100577444

Links

ENSG00000181458 ∙ NCBI:55076 ∙ OMIM:616928 ∙ HGNC:25480 ∙ Uniprot:Q9NWC5 ∙ 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 TMEM45A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM45A 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			12	3		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	3	0

Variants in TMEM45A

This is a list of pathogenic ClinVar variants found in the TMEM45A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-100555246-C-A		not specified	Uncertain significance (Jan 24, 2023)
3-100555274-G-C		not specified	Uncertain significance (Jun 18, 2021)
3-100555284-A-T		not specified	Likely benign (Jun 29, 2023)
3-100555350-T-A		not specified	Uncertain significance (Jul 10, 2024)
3-100555393-C-A		not specified	Uncertain significance (Aug 04, 2023)
3-100558437-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-100558440-A-G		not specified	Uncertain significance (Feb 15, 2023)
3-100558479-G-A		not specified	Likely benign (Oct 27, 2022)
3-100558501-C-A		not specified	Uncertain significance (Oct 11, 2024)
3-100558522-G-A		not specified	Uncertain significance (Nov 22, 2024)
3-100558549-G-T		not specified	Uncertain significance (Mar 02, 2023)
3-100558584-T-G		not specified	Uncertain significance (Jun 17, 2024)
3-100568852-G-A		not specified	Uncertain significance (May 23, 2023)
3-100568880-A-C		not specified	Uncertain significance (Dec 16, 2022)
3-100568928-C-A		not specified	Uncertain significance (Jan 22, 2024)
3-100568939-G-A		not specified	Likely benign (Apr 19, 2023)
3-100576935-T-G		not specified	Uncertain significance (Jun 12, 2023)
3-100576960-C-T		not specified	Uncertain significance (Apr 23, 2024)
3-100576972-T-G		not specified	Uncertain significance (Oct 02, 2023)
3-100576990-G-A		not specified	Uncertain significance (Jul 21, 2021)
3-100576995-C-A		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM45A	protein_coding	protein_coding	ENST00000323523	5	84826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00476	0.969	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.632	124	145	0.853	0.00000712	1791
Missense in Polyphen		24	36.547	0.65669		485
Synonymous	0.211	50	51.9	0.963	0.00000247	526
Loss of Function	1.94	6	13.8	0.435	7.37e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00427	0.00428
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0902

Intolerance Scores

• loftool: 0.646
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.253
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.754

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem45a

Gene ontology

• Cellular component: integral component of membrane