NEMF

nuclear export mediator factor

Basic information

Region (hg38): 14:49782082-49852821

Previous symbols: [ "SDCCAG1" ]

Links

ENSG00000165525 ∙ NCBI:9147 ∙ OMIM:608378 ∙ HGNC:10663 ∙ Uniprot:O60524 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with speech delay and axonal peripheral neuropathy	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	32934225; 33048237

ClinVar

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

• not provided (7 variants)
• Intellectual developmental disorder with speech delay and axonal peripheral neuropathy (2 variants)
• Inborn genetic diseases (2 variants)
• See cases (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				13	3	16
missense		1	56	4		61
nonsense	4	1				5
start loss	1		1			2
frameshift	6	3				9
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2				2
splice region			1	2	2	5
non coding			4		3	7
Total	11	7	62	17	6

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)
14-49782593-C-T		not specified	Uncertain significance (Dec 03, 2021)
14-49782879-T-C		not specified	Uncertain significance (May 17, 2023)
14-49782884-C-A		not specified	Uncertain significance (Oct 12, 2021)
14-49784672-C-A			Likely benign (Dec 01, 2022)
14-49784706-T-C		Inborn genetic diseases	Uncertain significance (Oct 27, 2022)
14-49784952-T-C		NEMF-related disorder	Benign (Dec 31, 2019)
14-49784959-G-A		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
14-49784975-G-A		Inborn genetic diseases	Uncertain significance (Jun 04, 2021)
14-49784976-C-T		Inborn genetic diseases	Uncertain significance (Jun 04, 2021)
14-49784977-A-G		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
14-49785262-G-A		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
14-49785298-GTCAAAGAA-G		Intellectual developmental disorder with speech delay and axonal peripheral neuropathy	Likely pathogenic (May 26, 2022)
14-49785313-A-G		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
14-49786722-T-A		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
14-49786729-G-C		Inborn genetic diseases	Uncertain significance (Feb 17, 2022)
14-49789165-T-C		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
14-49789165-T-TCTACA		Intellectual developmental disorder with speech delay and axonal peripheral neuropathy • See cases	Pathogenic (-)
14-49789196-T-C		Inborn genetic diseases	Likely benign (Jul 06, 2021)
14-49789209-C-T		NEMF-related disorder	Likely benign (Feb 20, 2019)
14-49789255-G-A		Inborn genetic diseases	Uncertain significance (Oct 02, 2023)
14-49789264-G-A			Likely pathogenic (Jul 12, 2020)
14-49789272-CT-C			Pathogenic (Apr 19, 2022)
14-49789512-A-G		Inborn genetic diseases	Uncertain significance (Apr 27, 2023)
14-49795791-CT-C		Intellectual developmental disorder with speech delay and axonal peripheral neuropathy	Pathogenic (Apr 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEMF	protein_coding	protein_coding	ENST00000298310	33	69925

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000358	1.00	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	470	548	0.857	0.0000267	7131
Missense in Polyphen		136	204.64	0.66459		2693
Synonymous	-1.13	202	183	1.11	0.00000924	1863
Loss of Function	5.63	21	72.9	0.288	0.00000399	900

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000615	0.000611
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000109	0.000109
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000250	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.000176	0.000163
Other	0.000165	0.000163

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

• 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

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

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