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GeneBe

NEMF

nuclear export mediator factor

Basic information

Region (hg38): 14:49782082-49852821

Previous symbols: [ "SDCCAG1" ]

Links

ENSG00000165525NCBI:9147OMIM:608378HGNC:10663Uniprot:O60524AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • intellectual developmental disorder with speech delay and axonal peripheral neuropathy (Strong), mode of inheritance: AR
  • intellectual developmental disorder with speech delay and axonal peripheral neuropathy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder with speech delay and axonal peripheral neuropathyARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal; Neurologic32934225; 33048237

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEMF gene.

  • Inborn genetic diseases (49 variants)
  • not provided (26 variants)
  • Intellectual developmental disorder with speech delay and axonal peripheral neuropathy (5 variants)
  • See cases (2 variants)
  • NEMF-related condition (1 variants)
  • Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEMF 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
5
clinvar
3
clinvar
8
missense
1
clinvar
43
clinvar
4
clinvar
48
nonsense
3
clinvar
1
clinvar
4
start loss
1
clinvar
1
clinvar
2
frameshift
6
clinvar
3
clinvar
9
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
1
1
2
non coding
4
clinvar
2
clinvar
6
Total 10 7 49 9 5

Highest pathogenic variant AF is 0.0000394

Variants in NEMF

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

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

Position Type Phenotype Significance ClinVar
14-49782395-G-A not specified Uncertain significance (Jul 09, 2021)2341262
14-49782593-C-T not specified Uncertain significance (Dec 03, 2021)2362976
14-49782879-T-C not specified Uncertain significance (May 17, 2023)2547555
14-49782884-C-A not specified Uncertain significance (Oct 12, 2021)2255084
14-49784672-C-A Likely benign (Dec 01, 2022)2644214
14-49784706-T-C Inborn genetic diseases Uncertain significance (Oct 27, 2022)2375362
14-49784952-T-C NEMF-related condition Benign (Dec 31, 2019)779679
14-49784959-G-A Inborn genetic diseases Uncertain significance (Nov 18, 2022)2328157
14-49784975-G-A Inborn genetic diseases Uncertain significance (Jun 04, 2021)2289211
14-49784976-C-T Inborn genetic diseases Uncertain significance (Jun 04, 2021)2289129
14-49784977-A-G Inborn genetic diseases Uncertain significance (Jun 13, 2023)2560123
14-49785262-G-A Inborn genetic diseases Uncertain significance (Mar 24, 2023)2529277
14-49785298-GTCAAAGAA-G Intellectual developmental disorder with speech delay and axonal peripheral neuropathy Likely pathogenic (May 26, 2022)2432191
14-49785313-A-G Inborn genetic diseases Uncertain significance (Sep 20, 2023)3193373
14-49786722-T-A Inborn genetic diseases Uncertain significance (Aug 12, 2021)2378696
14-49786729-G-C Inborn genetic diseases Uncertain significance (Feb 17, 2022)2220745
14-49789165-T-C Inborn genetic diseases Uncertain significance (Jan 09, 2024)3193364
14-49789165-T-TCTACA Intellectual developmental disorder with speech delay and axonal peripheral neuropathy • See cases Pathogenic (-)986402
14-49789196-T-C Inborn genetic diseases Likely benign (Jul 06, 2021)2235071
14-49789209-C-T NEMF-related condition Likely benign (Feb 20, 2019)3058114
14-49789255-G-A Inborn genetic diseases Uncertain significance (Oct 02, 2023)3193356
14-49789264-G-A Likely pathogenic (Jul 12, 2020)973823
14-49789272-CT-C Pathogenic (Apr 19, 2022)973828
14-49789512-A-G Inborn genetic diseases Uncertain significance (Apr 27, 2023)2562609
14-49795791-CT-C Intellectual developmental disorder with speech delay and axonal peripheral neuropathy Pathogenic (Apr 02, 2021)986403

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NEMFprotein_codingprotein_codingENST00000298310 3369925
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003581.001256890591257480.000235
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.194705480.8570.00002677131
Missense in Polyphen136204.640.664592693
Synonymous-1.132021831.110.000009241863
Loss of Function5.632172.90.2880.00000399900

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006150.000611
Ashkenazi Jewish0.0003980.000397
East Asian0.0001090.000109
Finnish0.0002780.000277
European (Non-Finnish)0.0002500.000246
Middle Eastern0.0001090.000109
South Asian0.0001760.000163
Other0.0001650.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation. NEMF is responsible for selective recognition of stalled 60S subunits by recognizing an exposed, nascent chain-conjugated tRNA moiety. NEMF is important for the stable association of LTN1 to the complex (PubMed:25578875). May indirectly play a role in nuclear export (PubMed:16103875). {ECO:0000269|PubMed:16103875, ECO:0000269|PubMed:25578875}.;

Intolerance Scores

loftool
rvis_EVS
-1.7
rvis_percentile_EVS
2.54

Haploinsufficiency Scores

pHI
0.951
hipred
Y
hipred_score
0.544
ghis
0.669

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nemf
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;

Gene ontology

Biological process
nuclear export;rescue of stalled ribosome;ribosome-associated ubiquitin-dependent protein catabolic process
Cellular component
nucleus;RQC complex
Molecular function
tRNA binding;ribosomal large subunit binding