LONRF3

protein-coding

LON peptidase N-terminal domain and ring finger 3, the group of Ring finger proteins

Gene summary

The protein encoded by this gene contains a RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Multiple alternatively spliced transcript variants have been suggested, but their full length natures are not clear. [provided by RefSeq, Jul 2008]

Previous symbols:

RNF127

MANE transcript

NM_001031855.3

Inheritance

—

ClinVar variants

U:160B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chrX:118,974,614-119,022,925

External References & Databases

Ensembl (ENSG00000175556)

Transcript & Mutation Effects

hg38 • Region Span ~48.3 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 LONRF3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031855.3. 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			4 clinvar	4 clinvar		8
missense			124 clinvar	4 clinvar		128
nonsense			10 clinvar			10
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			22 clinvar			22
Total	0	0	160	8	0	168

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031855.3	RefSeq	NP_001027026.1	11	MANE Select
ENST00000371628.8	Ensembl	ENSP00000360690.3	11	MANE Select
NM_001289109.1	RefSeq	NP_001276038.1	11	Standard
NM_024778.5	RefSeq	NP_079054.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371628
Coding exons: 11
Length: 43738
Individuals with no LoFs: 125686
Homozygous LoFs: 1
Heterozygous LoFs: 3
Defined: 125690
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	224	284	0.788	0.0000212	4901
Missense (PolyPhen)		73	138.15	0.5284		2294
Synonymous	-0.518	122	115	1.06	0.00000870	1506
Loss of Function	3.44	5	22.7	0.220	0.00000160	418

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000045	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000018	rare
South Asian	0	0.0	absent
Other	0.00023	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.214
RVIS EVS: -0.16
RVIS percentile EVS: 42.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0493

Gene Damage Prediction

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