TRAM1L1

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

Basic information

Region (hg38): 4:117083554-117085576

Links

ENSG00000174599 ∙ NCBI:133022 ∙ OMIM:617505 ∙ HGNC:28371 ∙ Uniprot:Q8N609 ∙ 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 TRAM1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAM1L1 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				1	1	2
missense			15	1		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	15	2	1

Variants in TRAM1L1

This is a list of pathogenic ClinVar variants found in the TRAM1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-117084302-C-T			Benign (Oct 09, 2018)
4-117084318-T-G		not specified	Uncertain significance (Feb 22, 2023)
4-117084328-T-C		not specified	Uncertain significance (May 01, 2024)
4-117084410-A-G			Likely benign (Dec 01, 2022)
4-117084586-G-A		not specified	Uncertain significance (Dec 31, 2023)
4-117084589-C-T		not specified	Uncertain significance (Aug 02, 2022)
4-117084603-G-A		not specified	Uncertain significance (Oct 04, 2022)
4-117084669-C-T		not specified	Uncertain significance (May 18, 2022)
4-117084697-A-C		not specified	Uncertain significance (Sep 27, 2021)
4-117084796-T-A		not specified	Uncertain significance (Dec 28, 2023)
4-117084819-T-C		not specified	Uncertain significance (Oct 26, 2021)
4-117084843-T-C		not specified	Uncertain significance (Aug 14, 2023)
4-117084891-A-G		not specified	Uncertain significance (Dec 19, 2022)
4-117084948-G-T		not specified	Uncertain significance (Apr 23, 2024)
4-117085051-T-C		not specified	Uncertain significance (Sep 22, 2023)
4-117085074-T-C		not specified	Likely benign (Jun 05, 2023)
4-117085215-G-T		not specified	Uncertain significance (Dec 05, 2022)
4-117085218-A-T		not specified	Uncertain significance (Oct 12, 2021)
4-117085285-C-G		not specified	Uncertain significance (Mar 01, 2023)
4-117085377-T-C		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAM1L1	protein_coding	protein_coding	ENST00000310754	1	2019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00664	0.768	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.239	191	201	0.952	0.0000101	2424
Missense in Polyphen		47	49.187	0.95553		701
Synonymous	0.482	74	79.5	0.931	0.00000441	723
Loss of Function	0.905	4	6.49	0.617	2.75e-7	86

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulatory or required for the translocation of secretory proteins across the ER membrane. {ECO:0000250}.

Recessive Scores

• pRec: 0.0858

Intolerance Scores

• loftool: 0.469
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.0826
• hipred: N
• hipred_score: 0.112
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tram1l1

Gene ontology

• Biological process: SRP-dependent cotranslational protein targeting to membrane, translocation
• Cellular component: endoplasmic reticulum membrane;rough endoplasmic reticulum;integral component of membrane