NEMF
Basic information
Region (hg38): 14:49782083-49852821
Previous symbols: [ "SDCCAG1" ]
Links
Phenotypes
GenCC
Source:
- 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:
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
- 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 | 16 | ||||
missense | 56 | 61 | ||||
nonsense | 5 | |||||
start loss | 2 | |||||
frameshift | 9 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 2 | 2 | 5 | ||
non coding | 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) | ||
14-49789237-A-T | Inborn genetic diseases | Uncertain significance (Mar 19, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
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