NARF

protein-coding

nuclear prelamin A recognition factor

Gene summary

Several proteins have been found to be prenylated and methylated at their carboxyl-terminal ends. Prenylation was initially believed to be important only for membrane attachment. However, another role for prenylation appears to be its importance in protein-protein interactions. The only nuclear proteins known to be prenylated in mammalian cells are prelamin A- and B-type lamins. Prelamin A is farnesylated and carboxymethylated on the cysteine residue of a carboxyl-terminal CaaX motif. This post-translationally modified cysteine residue is removed from prelamin A when it is endoproteolytically processed into mature lamin A. The protein encoded by this gene binds to the prenylated prelamin A carboxyl-terminal tail domain. It may be a component of a prelamin A endoprotease complex. The encoded protein is located in the nucleus, where it partially colocalizes with the nuclear lamina. It shares limited sequence similarity with iron-only bacterial hydrogenases. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene, including one with a novel exon that is generated by RNA editing. [provided by RefSeq, Jul 2008]

MANE transcript

NM_012336.4

Inheritance

—

ClinVar variants

U:78B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr17:82,458,180-82,490,537

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~32.4 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 NARF variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 79
not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012336.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
76
clinvar
5
clinvar
81
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00786084
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_012336.4RefSeqNP_036468.111MANE Select
ENST00000309794.16EnsemblENSP00000309899.1011MANE Select
NM_001038618.3RefSeqNP_001033707.19Standard
NM_001083608.2RefSeqNP_001077077.110Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

  • lamin binding

Cellular Component

  • nucleus
  • lamin filament
  • nuclear lamina
  • nucleolus
  • nuclear lumen

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000309794
Coding exons
11
Length
32358
Individuals with no LoFs
125697
Homozygous LoFs
0
Heterozygous LoFs
51
Defined
125748
p
0.000203
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.03782792771.010.00001682990
Missense (PolyPhen)6570.6790.91965954
Synonymous0.01341121120.9980.00000733863
Loss of Function0.5032022.60.8860.00000118274

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000210.00020rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000660.00065rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000180.00018rare
South Asian0.000230.00023rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.100

Intolerance Scores

LoFtool
0.891
RVIS EVS
-1.15
RVIS percentile EVS
6.23

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.962

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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