TRIM16

tripartite motif containing 16, the group of Tripartite motif family

Basic information

Region (hg38): 17:15627959-15684311

Links

ENSG00000221926 ∙ NCBI:10626 ∙ OMIM:609505 ∙ HGNC:17241 ∙ Uniprot:O95361 ∙ 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 TRIM16 gene.

• Inborn genetic diseases (22 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM16 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			17	4	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	19	4	1

Variants in TRIM16

This is a list of pathogenic ClinVar variants found in the TRIM16 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-15628628-C-A			Benign (Apr 17, 2018)
17-15628707-A-G		not specified	Uncertain significance (Feb 28, 2023)
17-15628766-G-A		not specified	Uncertain significance (Dec 09, 2023)
17-15628796-A-C		not specified	Uncertain significance (Jan 08, 2024)
17-15628832-C-T		not specified	Uncertain significance (Jul 11, 2023)
17-15628938-T-C		not specified	Uncertain significance (Sep 22, 2023)
17-15628988-T-A		not specified	Uncertain significance (May 06, 2022)
17-15629064-G-A		not specified	Uncertain significance (Jul 19, 2023)
17-15629085-G-A		not specified	Uncertain significance (Jan 25, 2024)
17-15629114-G-T		not specified	Uncertain significance (Nov 22, 2021)
17-15629127-C-A		not specified	Uncertain significance (Sep 27, 2022)
17-15631636-C-G		not specified	Uncertain significance (Nov 13, 2023)
17-15631669-T-C		not specified	Uncertain significance (Dec 19, 2022)
17-15631696-G-A		not specified	Uncertain significance (Nov 08, 2021)
17-15632565-T-C		not specified	Uncertain significance (Aug 16, 2022)
17-15632577-T-C		not specified	Uncertain significance (Dec 13, 2022)
17-15636073-C-G			Likely benign (Dec 01, 2022)
17-15636083-C-T		not specified	Uncertain significance (Mar 22, 2023)
17-15636088-T-A		not specified	Uncertain significance (Sep 28, 2022)
17-15636124-T-C		not specified	Uncertain significance (Jun 21, 2022)
17-15636164-C-T		not specified	Uncertain significance (Aug 03, 2022)
17-15636265-G-A		not specified	Uncertain significance (Jan 05, 2022)
17-15642733-T-G		not specified	Likely benign (Nov 06, 2023)
17-15642755-A-G		not specified	Uncertain significance (Jun 18, 2021)
17-15642767-T-A		not specified	Uncertain significance (Oct 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM16	protein_coding	protein_coding	ENST00000578237	6	56352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.16e-9	0.516	125445	1	302	125748	0.00121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.336	300	317	0.947	0.0000180	3716
Missense in Polyphen		112	95.544	1.1722		1131
Synonymous	1.10	116	132	0.878	0.00000807	1068
Loss of Function	1.10	16	21.5	0.743	0.00000100	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000774	0.000757
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00816	0.00819
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000400	0.000360
Middle Eastern	0.00816	0.00819
South Asian	0.00297	0.00291
Other	0.000656	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of keratinocyte differentiation.

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.440

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim16

Gene ontology

• Biological process: response to retinoic acid;histone H3 acetylation;histone H4 acetylation;positive regulation of keratinocyte differentiation;positive regulation of transcription, DNA-templated;response to organophosphorus;positive regulation of retinoic acid receptor signaling pathway;positive regulation of interleukin-1 beta secretion;response to growth hormone
• Cellular component: cytoplasm;cytosol;plasma membrane;PML body
• Molecular function: DNA binding;protein binding;zinc ion binding;transferase activity;interleukin-1 binding;NACHT domain binding