RNFT1

ring finger protein, transmembrane 1, the group of Ring finger proteins

Basic information

Region (hg38): 17:59952239-59964761

Links

ENSG00000189050 ∙ NCBI:51136 ∙ OMIM:615172 ∙ HGNC:30206 ∙ Uniprot:Q5M7Z0 ∙ 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 RNFT1 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNFT1 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				1		1
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in RNFT1

This is a list of pathogenic ClinVar variants found in the RNFT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-59952983-T-C		not specified	Uncertain significance (Oct 12, 2022)
17-59953024-T-C		not specified	Uncertain significance (Feb 12, 2024)
17-59953065-T-C		not specified	Uncertain significance (Oct 25, 2023)
17-59954062-T-C		not specified	Likely benign (Feb 16, 2023)
17-59954097-A-G		not specified	Uncertain significance (Jan 26, 2022)
17-59954116-A-G		not specified	Uncertain significance (Nov 08, 2022)
17-59957342-T-C		not specified	Uncertain significance (Nov 30, 2022)
17-59957354-A-G		not specified	Uncertain significance (Jan 23, 2023)
17-59958388-A-G		not specified	Uncertain significance (May 27, 2022)
17-59958416-G-A		not specified	Uncertain significance (May 06, 2022)
17-59960147-A-G		not specified	Uncertain significance (Dec 27, 2023)
17-59960156-T-C		not specified	Uncertain significance (Dec 02, 2022)
17-59962562-A-G		not specified	Uncertain significance (Sep 13, 2023)
17-59962829-G-A		not specified	Uncertain significance (Jan 04, 2024)
17-59962854-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-59962908-G-A		not specified	Uncertain significance (Aug 02, 2022)
17-59962944-A-C		not specified	Uncertain significance (Mar 29, 2022)
17-59962995-G-A		not specified	Uncertain significance (Dec 15, 2022)
17-59963097-G-C		not specified	Uncertain significance (Sep 28, 2022)
17-59963136-C-T		not specified	Uncertain significance (Jun 11, 2021)
17-59963150-T-C		not specified	Uncertain significance (Mar 05, 2024)
17-59963162-G-C		not specified	Uncertain significance (Aug 08, 2023)
17-59963165-G-T		not specified	Uncertain significance (Jun 24, 2022)
17-59963174-T-C		not specified	Uncertain significance (Dec 11, 2023)
17-59963203-G-A			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNFT1	protein_coding	protein_coding	ENST00000305783	9	12522

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000109	0.943	125621	1	126	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.663	197	225	0.876	0.0000108	2830
Missense in Polyphen		51	55.033	0.92672		764
Synonymous	1.32	62	76.7	0.809	0.00000359	812
Loss of Function	1.83	13	22.3	0.582	0.00000112	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00293	0.00281
Ashkenazi Jewish	0.00	0.00
East Asian	0.000336	0.000326
Finnish	0.0000981	0.0000924
European (Non-Finnish)	0.000466	0.000448
Middle Eastern	0.000336	0.000326
South Asian	0.000136	0.000131
Other	0.000654	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that acts in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which targets misfolded proteins that accumulate in the endoplasmic reticulum (ER) for ubiquitination and subsequent proteasome- mediated degradation. Protects cells from ER stress-induced apoptosis. {ECO:0000269|PubMed:27485036}.

Recessive Scores

• pRec: 0.0942

Intolerance Scores

• loftool: 0.766
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.0821
• hipred: N
• hipred_score: 0.443
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.489

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnft1

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: transferase activity;metal ion binding