TRIM39-RPP21

TRIM39-RPP21 readthrough

Basic information

Region (hg38): 6:30328906-30346854

Links

ENSG00000248167 ∙ NCBI:202658 ∙ ∙ HGNC:38845 ∙ ∙ ∙ 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 TRIM39-RPP21 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM39-RPP21 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	2		7
Total	0	0	5	2	0

Variants in TRIM39-RPP21

This is a list of pathogenic ClinVar variants found in the TRIM39-RPP21 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30340273-A-C		not specified	Likely benign (Aug 10, 2023)
6-30340279-C-T		not specified	Likely benign (Dec 21, 2022)
6-30340318-C-T		not specified	Uncertain significance (Dec 09, 2023)
6-30340333-C-T		not specified	Likely benign (Dec 18, 2023)
6-30341823-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-30341942-G-A		not specified	Uncertain significance (Apr 11, 2023)
6-30342080-A-G		not specified	Likely benign (Jan 30, 2024)
6-30342132-G-A		not specified	Uncertain significance (Oct 06, 2022)
6-30342233-A-G		not specified	Uncertain significance (May 18, 2022)
6-30345481-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM39-RPP21	protein_coding	protein_coding	ENST00000513556	10	17273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.744	0.256	125704	0	10	125714	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	147	249	0.591	0.0000147	2685
Missense in Polyphen		11	39.718	0.27695		420
Synonymous	1.13	80	93.9	0.852	0.00000484	817
Loss of Function	3.87	5	26.5	0.189	0.00000164	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000894	0.0000894
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000477	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000665	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Haploinsufficiency Scores

• ghis: 0.419

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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