TRIM71

tripartite motif containing 71, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 3:32817996-32897824

Links

ENSG00000206557 ∙ NCBI:131405 ∙ OMIM:618570 ∙ HGNC:32669 ∙ Uniprot:Q2Q1W2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hydrocephalus, congenital communicating, 1 (Limited), mode of inheritance: AD
• hydrocephalus, congenital communicating, 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hydrocephalus, congenital, 4	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	29983323

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM71 gene.

• Inborn genetic diseases (22 variants)
• not provided (12 variants)
• Non-obstructive azoospermia (8 variants)
• Hydrocephalus, congenital communicating, 1 (7 variants)
• Cryptozoospermia (3 variants)
• Congenital hydrocephalus (1 variants)
• TRIM71-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM71 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				5	2	7
missense			36	3		39
nonsense						0
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	1	38	8	2

Variants in TRIM71

This is a list of pathogenic ClinVar variants found in the TRIM71 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-32818093-C-G		not specified	Uncertain significance (May 17, 2023)
3-32818179-G-C		TRIM71-related disorder	Likely benign (Feb 24, 2023)
3-32818199-C-T		not specified	Uncertain significance (Mar 31, 2023)
3-32818279-C-A		Hydrocephalus, congenital communicating, 1 • not specified	Uncertain significance (Mar 02, 2023)
3-32818299-C-CCGGCTGCCGGCGGCGGG		Non-obstructive azoospermia	Likely pathogenic (Mar 01, 2021)
3-32818310-C-G		not specified	Uncertain significance (May 30, 2022)
3-32818317-C-T			Likely benign (Jul 16, 2018)
3-32818328-C-T		Cryptozoospermia	Uncertain significance (Mar 01, 2021)
3-32818419-C-T		TRIM71-related disorder	Likely benign (Jun 07, 2022)
3-32818448-T-C		Cryptozoospermia	Uncertain significance (Mar 01, 2021)
3-32818454-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-32818489-G-GCCGGCGCT		Hydrocephalus, congenital communicating, 1	Uncertain significance (Dec 28, 2021)
3-32818535-A-C		not specified	Uncertain significance (Jul 13, 2022)
3-32818538-C-T		not specified	Uncertain significance (Sep 29, 2023)
3-32818565-C-T		not specified	Uncertain significance (Jul 12, 2023)
3-32818633-G-T		Non-obstructive azoospermia	Likely benign (Mar 01, 2021)
3-32818643-C-A		not specified	Uncertain significance (Sep 27, 2021)
3-32818663-C-A		not specified	Uncertain significance (Jan 06, 2023)
3-32818702-G-A		not specified	Uncertain significance (Nov 21, 2022)
3-32818787-A-G		TRIM71-related disorder	Likely pathogenic (Feb 09, 2024)
3-32818817-G-C		not specified	Likely benign (Apr 07, 2023)
3-32818851-G-A		TRIM71-related disorder	Likely benign (Nov 01, 2022)
3-32818856-C-G		not specified	Uncertain significance (Oct 27, 2023)
3-32818865-G-C		Non-obstructive azoospermia	Likely benign (Mar 01, 2021)
3-32818883-T-A		Non-obstructive azoospermia	Uncertain significance (Mar 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM71	protein_coding	protein_coding	ENST00000383763	4	79809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000310	112519	0	1	112520	0.00000444

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.28	295	502	0.588	0.0000305	5581
Missense in Polyphen		31	158.33	0.1958		1537
Synonymous	-3.53	294	226	1.30	0.0000142	1867
Loss of Function	4.69	1	27.6	0.0363	0.00000164	265

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)	0.0000101	0.0000101
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that cooperates with the microRNAs (miRNAs) machinery and promotes embryonic stem cells proliferation and maintenance (Probable). Binds to miRNAs and associates with AGO2, participating in post-transcriptional repression of transcripts such as CDKN1A (By similarity). In addition, participates in post-transcriptional mRNA repression in a miRNA independent mechanism (PubMed:23125361). Facilitates the G1-S transition to promote rapid embryonic stem cell self-renewal by repressing CDKN1A expression. Required to maintain proliferation and prevent premature differentiation of neural progenitor cells during early neural development: positively regulates FGF signaling by controlling the stability of SHCBP1 (By similarity). Specific regulator of miRNA biogenesis. Binds to miRNA MIR29A hairpin and postranscriptionally modulates MIR29A levels, which indirectly regulates TET proteins expression (PubMed:28431233). {ECO:0000250|UniProtKB:Q1PSW8, ECO:0000269|PubMed:23125361, ECO:0000269|PubMed:28431233, ECO:0000305|PubMed:24239284}.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);Mesodermal Commitment Pathway;let-7 inhibition of ES cell reprogramming;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.00448
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.43

Haploinsufficiency Scores

• pHI: 0.379
• hipred: Y
• hipred_score: 0.728
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.512

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim71
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: trim71
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: sigmoid

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;protein polyubiquitination;neural tube closure;fibroblast growth factor receptor signaling pathway;miRNA metabolic process;posttranscriptional regulation of gene expression;negative regulation of translation;neural tube development;production of miRNAs involved in gene silencing by miRNA;miRNA mediated inhibition of translation;proteasome-mediated ubiquitin-dependent protein catabolic process;protein autoubiquitination;regulation of gene silencing by miRNA;3'-UTR-mediated mRNA destabilization;stem cell proliferation;regulation of neural precursor cell proliferation;positive regulation of gene silencing by miRNA
• Cellular component: P-body
• Molecular function: ubiquitin-protein transferase activity;protein binding;zinc ion binding;translation repressor activity;miRNA binding;ubiquitin protein ligase activity