RNFT2

protein-coding

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

Gene summary

Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in positive regulation of ERAD pathway. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TMEM118

MANE transcript

NM_001382266.1

Inheritance

—

ClinVar variants

U:66

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr12:116,738,178-116,853,631

External References & Databases

Ensembl (ENSG00000135119)

Transcript & Mutation Effects

hg38 • Region Span ~115.5 kb

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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 RNFT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001382266.1. 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						0
missense			64 clinvar			64
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	66	0	0	66

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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_001382266.1	RefSeq	NP_001369195.1	10	MANE Select
ENST00000257575.9	Ensembl	ENSP00000257575.4	10	MANE Select
NM_001109903.2	RefSeq	NP_001103373.1	10	Standard
NM_032814.4	RefSeq	NP_116203.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

metal ion binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257575
Coding exons: 10
Length: 115341
Individuals with no LoFs: 125572
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125593
p: 0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	171	263	0.651	0.0000161	2810
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00012	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00024	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.412
RVIS EVS: -0.8
RVIS percentile EVS: 12.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.604

Gene Damage Prediction

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