TRIM31

protein-coding

tripartite motif containing 31, the group of Tripartite motif family|Ring finger proteins

Gene summary

This gene encodes a protein that functions as an E3 ubiquitin-protein ligase. This gene shows altered expression in certain tumors and may be a negative regulator of cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

MANE transcript

NM_007028.5

Inheritance

—

ClinVar variants

U:53B:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr6:30,102,897-30,113,090

External References & Databases

Ensembl (ENSG00000204616)

Transcript & Mutation Effects

hg38 • Region Span ~10.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRIM31 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007028.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			52 clinvar	6 clinvar	7 clinvar	65
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	9	8	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007028.5	RefSeq	NP_008959.3	8	MANE Select
ENST00000376734.4	Ensembl	ENSP00000365924.3	8	MANE Select
ENST00000873799.1	Ensembl	ENSP00000543858.1	8	Standard
ENST00000873799.2	Ensembl	ENSP00000543858.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cytokine Signaling in Immune system
Immune System
Interferon gamma signaling
Interferon Signaling

Biological Process

protein ubiquitination
negative regulation of viral transcription
innate immune response
negative regulation of viral entry into host cell
positive regulation of DNA-binding transcription factor activity

Molecular Function

protein binding
zinc ion binding
transferase activity

Cellular Component

mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376734
Coding exons: 8
Length: 10210
Individuals with no LoFs: 125700
Homozygous LoFs: 1
Heterozygous LoFs: 47
Defined: 125748
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.346	205	219	0.934	0.0000110	2806
Missense (PolyPhen)		36	37.567	0.95829		546
Synonymous	1.41	75	92.2	0.813	0.00000508	782
Loss of Function	1.43	11	17.5	0.630	7.38e-7	217

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000082	0.000079	rare
South Asian	0.00077	0.00069	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulator of Src-induced anchorage independent cell growth (By similarity). May have E3 ubiquitin-protein ligase activity. {ECO:0000250, ECO:0000269|PubMed:18773414}.;

Intolerance Scores

LoFtool: 0.561
RVIS EVS: 2.98
RVIS percentile EVS: 99.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.787

Gene Damage Prediction

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