NGDN

neuroguidin, the group of SSU processome

Basic information

Region (hg38): 14:23469679-23509862

Previous symbols: [ "C14orf120" ]

Links

ENSG00000129460NCBI:25983OMIM:610777HGNC:20271Uniprot:Q8NEJ9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NGDN 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
0
missense
17
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 17 0 0

Variants in NGDN

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

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

Position Type Phenotype Significance ClinVar
14-23470088-A-G not specified Uncertain significance (Jan 16, 2024)3198947
14-23470090-C-T not specified Uncertain significance (Oct 20, 2021)2306657
14-23470927-G-A not specified Uncertain significance (Aug 20, 2024)3405325
14-23470966-C-T not specified Uncertain significance (Dec 03, 2024)3405330
14-23475177-A-G not specified Uncertain significance (Feb 23, 2023)2469093
14-23475211-T-C not specified Uncertain significance (Aug 14, 2023)2599370
14-23475275-T-A not specified Uncertain significance (Jun 19, 2024)3299600
14-23475743-C-G not specified Uncertain significance (Aug 17, 2021)2246139
14-23476064-A-T not specified Uncertain significance (Nov 10, 2024)3405329
14-23476107-G-A not specified Uncertain significance (Sep 20, 2023)3198936
14-23476143-G-A not specified Uncertain significance (Jun 18, 2024)3299599
14-23476289-C-T not specified Uncertain significance (Jan 24, 2023)2461065
14-23476355-C-T not specified Uncertain significance (Dec 03, 2024)3405331
14-23476374-A-C not specified Uncertain significance (Jul 10, 2024)3405327
14-23476374-A-G not specified Uncertain significance (Feb 14, 2023)2483687
14-23476374-A-T not specified Uncertain significance (Sep 02, 2024)3405328
14-23476383-G-A not specified Uncertain significance (Nov 15, 2024)3405324
14-23476404-A-G not specified Uncertain significance (Feb 05, 2024)3198955
14-23477207-T-C not specified Uncertain significance (Jan 23, 2023)2477989
14-23477279-A-G not specified Uncertain significance (Oct 13, 2023)3198960
14-23477311-C-A not specified Uncertain significance (Sep 21, 2023)3198966
14-23477346-A-G not specified Uncertain significance (Aug 17, 2022)2308109
14-23477524-C-T not specified Uncertain significance (May 18, 2023)2511957
14-23477548-C-G not specified Uncertain significance (Feb 12, 2024)3198970
14-23478013-G-A not specified Uncertain significance (May 30, 2023)2558248

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NGDNprotein_codingprotein_codingENST00000408901 1140175
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.04e-80.68012563201151257470.000457
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.02361901910.9950.00001172053
Missense in Polyphen4352.420.82029612
Synonymous-0.3956359.11.070.00000265597
Loss of Function1.281521.40.7020.00000127238

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004850.000485
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00004620.0000462
European (Non-Finnish)0.0006690.000668
Middle Eastern0.0001090.000109
South Asian0.0007840.000784
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in the translational repression of cytoplasmic polyadenylation element (CPE)-containing mRNAs. {ECO:0000250}.;

Recessive Scores

pRec
0.158

Intolerance Scores

loftool
0.963
rvis_EVS
-0.22
rvis_percentile_EVS
37.43

Haploinsufficiency Scores

pHI
0.128
hipred
N
hipred_score
0.442
ghis
0.588

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
N
gene_indispensability_score
0.486

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ngdn
Phenotype

Gene ontology

Biological process
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);regulation of translation
Cellular component
chromosome, centromeric region;nucleus;nucleolus;mitochondrion;filopodium;axon;dendrite;small-subunit processome
Molecular function
RNA binding;protein binding