RNFT2

ring finger protein, transmembrane 2, the group of Ring finger proteins

Basic information

Region (hg38): 12:116738177-116853631

Previous symbols: [ "TMEM118" ]

Links

ENSG00000135119 ∙ NCBI:84900 ∙ OMIM:620254 ∙ HGNC:25905 ∙ Uniprot:Q96EX2 ∙ 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 RNFT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNFT2 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in RNFT2

This is a list of pathogenic ClinVar variants found in the RNFT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-116740503-G-T		not specified	Uncertain significance (Jan 09, 2024)
12-116749846-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-116749855-C-T		not specified	Uncertain significance (May 03, 2023)
12-116749870-C-T		not specified	Uncertain significance (May 11, 2022)
12-116749968-T-G		not specified	Uncertain significance (Apr 08, 2024)
12-116750001-G-C		not specified	Uncertain significance (Apr 05, 2023)
12-116750115-G-A		not specified	Uncertain significance (Feb 23, 2023)
12-116750118-C-T		not specified	Uncertain significance (Dec 17, 2023)
12-116750173-A-T		not specified	Uncertain significance (Jul 13, 2022)
12-116750184-G-A		not specified	Uncertain significance (Oct 06, 2021)
12-116750283-A-G		not specified	Uncertain significance (Dec 16, 2021)
12-116754019-G-A		not specified	Uncertain significance (Mar 06, 2023)
12-116766871-C-G		not specified	Uncertain significance (Feb 02, 2024)
12-116779236-T-C		not specified	Uncertain significance (Jan 26, 2023)
12-116779251-T-C		not specified	Uncertain significance (Oct 27, 2022)
12-116779324-G-C		not specified	Uncertain significance (Dec 21, 2023)
12-116833874-T-C		not specified	Uncertain significance (Feb 26, 2024)
12-116835961-C-G		not specified	Uncertain significance (Jan 29, 2024)
12-116835975-G-A		not specified	Uncertain significance (Jan 04, 2024)
12-116835976-G-A		not specified	Uncertain significance (Jun 03, 2022)
12-116836194-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-116836202-G-A		not specified	Uncertain significance (Feb 13, 2024)
12-116836223-G-A		not specified	Uncertain significance (Nov 03, 2022)
12-116836250-G-A		not specified	Uncertain significance (Dec 12, 2023)
12-116849324-G-C		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNFT2	protein_coding	protein_coding	ENST00000257575	10	115341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000120	0.990	125572	0	21	125593	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	171	263	0.651	0.0000161	2810
Missense in Polyphen		40	78.935	0.50675		851
Synonymous	0.882	109	121	0.898	0.00000847	887
Loss of Function	2.30	12	24.2	0.496	0.00000135	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000430	0.000306
Ashkenazi Jewish	0.00	0.00
East Asian	0.000244	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.0000725	0.0000705
Middle Eastern	0.000244	0.000218
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.412
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

• pHI: 0.173
• hipred: Y
• hipred_score: 0.565
• ghis: 0.644

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.604

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnft2

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: metal ion binding