TRAM1

translocation associated membrane protein 1, the group of TLC domain containing

Basic information

Region (hg38): 8:70573218-70608416

Links

ENSG00000067167 ∙ NCBI:23471 ∙ OMIM:605190 ∙ HGNC:20568 ∙ Uniprot:Q15629 ∙ 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 TRAM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAM1 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			11	3	1	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	11	3	1

Variants in TRAM1

This is a list of pathogenic ClinVar variants found in the TRAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-70583178-G-T		not specified	Uncertain significance (Mar 14, 2023)
8-70583211-T-C		not specified	Uncertain significance (Feb 23, 2023)
8-70583299-C-T		not specified	Likely benign (Aug 13, 2021)
8-70583316-A-G		not specified	Uncertain significance (Dec 18, 2023)
8-70583662-A-G		not specified	Uncertain significance (Dec 20, 2023)
8-70586905-A-G		not specified	Uncertain significance (Apr 06, 2024)
8-70586947-G-T		not specified	Uncertain significance (Dec 09, 2023)
8-70587125-C-T		not specified	Uncertain significance (Oct 26, 2021)
8-70594525-T-C		not specified	Uncertain significance (May 09, 2023)
8-70594568-T-C		not specified	Uncertain significance (Jun 13, 2022)
8-70596318-T-C			Benign (Apr 06, 2018)
8-70597911-G-A		not specified	Uncertain significance (Apr 27, 2023)
8-70597921-C-T		not specified	Likely benign (Jun 24, 2022)
8-70598157-C-T		not specified	Likely benign (Mar 29, 2023)
8-70598189-A-C		not specified	Uncertain significance (Aug 08, 2022)
8-70608106-T-C		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAM1	protein_coding	protein_coding	ENST00000262213	11	34946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.925	0.0749	125733	0	6	125739	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	134	194	0.689	0.00000956	2452
Missense in Polyphen		20	58.017	0.34472		820
Synonymous	-1.58	85	68.3	1.24	0.00000339	705
Loss of Function	3.70	3	21.5	0.140	0.00000114	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulatory or required for the translocation of secretory proteins across the ER membrane. {ECO:0000269|PubMed:1315422}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;TLR4 Signaling and Tolerance;SRP-dependent cotranslational protein targeting to membrane;Translation;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.203
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.363
• hipred: Y
• hipred_score: 0.651
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tram1

Gene ontology

• Biological process: cotranslational protein targeting to membrane;SRP-dependent cotranslational protein targeting to membrane, translocation;viral process
• Cellular component: endoplasmic reticulum;rough endoplasmic reticulum;integral component of membrane;integral component of endoplasmic reticulum membrane
• Molecular function: protein binding;signaling receptor activity