TRAM2

translocation associated membrane protein 2, the group of TLC domain containing

Basic information

Region (hg38): 6:52497408-52577060

Links

ENSG00000065308 ∙ NCBI:9697 ∙ OMIM:608485 ∙ HGNC:16855 ∙ Uniprot:Q15035 ∙ 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 TRAM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAM2 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in TRAM2

This is a list of pathogenic ClinVar variants found in the TRAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-52503222-C-T		not specified	Uncertain significance (Aug 06, 2024)
6-52503225-G-A		not specified	Uncertain significance (Sep 07, 2022)
6-52503231-G-A		not specified	Uncertain significance (Apr 23, 2024)
6-52503253-C-T		not specified	Uncertain significance (Jun 12, 2023)
6-52504617-G-A		not specified	Uncertain significance (Dec 14, 2023)
6-52504629-G-A		not specified	Uncertain significance (Nov 09, 2024)
6-52504633-C-T		not specified	Uncertain significance (Aug 27, 2024)
6-52504660-C-T		not specified	Uncertain significance (Nov 08, 2024)
6-52504684-G-A		not specified	Uncertain significance (Dec 07, 2024)
6-52504704-C-T		not specified	Uncertain significance (Mar 30, 2024)
6-52504705-G-A		not specified	Uncertain significance (Feb 26, 2024)
6-52504726-C-T		not specified	Uncertain significance (Apr 25, 2023)
6-52505630-C-T		not specified	Uncertain significance (Aug 06, 2024)
6-52505642-C-A		not specified	Uncertain significance (May 26, 2024)
6-52505675-T-C		not specified	Uncertain significance (Mar 01, 2024)
6-52505684-C-G		not specified	Uncertain significance (Dec 13, 2023)
6-52505684-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-52506095-G-A		not specified	Uncertain significance (May 20, 2024)
6-52506100-C-A		not specified	Uncertain significance (Mar 18, 2024)
6-52506116-A-C		not specified	Uncertain significance (Mar 31, 2024)
6-52506128-C-T		not specified	Uncertain significance (Jan 30, 2024)
6-52506136-G-A		not specified	Likely benign (Dec 05, 2024)
6-52507610-C-T		not specified	Uncertain significance (Jul 23, 2024)
6-52509577-A-C		not specified	Uncertain significance (Oct 01, 2024)
6-52516053-C-T		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAM2	protein_coding	protein_coding	ENST00000182527	11	79514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.944	0.0558	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	145	218	0.665	0.0000125	2412
Missense in Polyphen		44	82.568	0.53289		958
Synonymous	0.284	83	86.4	0.961	0.00000489	710
Loss of Function	3.79	3	22.3	0.134	0.00000105	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for collagen type I synthesis. May couple the activity of the ER Ca(2+) pump SERCA2B with the activity of the translocon. This coupling may increase the local Ca(2+) concentration at the site of collagen synthesis, and a high Ca(2+) concentration may be necessary for the function of molecular chaperones involved in collagen folding. Required for proper insertion of the first transmembrane helix N-terminus of TM4SF20 into the ER lumen, may act as a ceramide sensor for regulated alternative translocation (RAT) (PubMed:27499293). {ECO:0000269|PubMed:14749390, ECO:0000269|PubMed:27499293}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0398
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.469
• hipred: Y
• hipred_score: 0.717
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.480

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tram2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; skeleton phenotype; immune system phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: SRP-dependent cotranslational protein targeting to membrane, translocation;collagen biosynthetic process;protein insertion into ER membrane
• Cellular component: rough endoplasmic reticulum;integral component of membrane
• Molecular function: protein binding