NGDN

neuroguidin, the group of SSU processome

Basic information

Region (hg38): 14:23469679-23509862

Previous symbols: [ "C14orf120" ]

Links

ENSG00000129460 ∙ NCBI:25983 ∙ OMIM:610777 ∙ HGNC:20271 ∙ Uniprot:Q8NEJ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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			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)
14-23470090-C-T		not specified	Uncertain significance (Oct 20, 2021)
14-23470927-G-A		not specified	Uncertain significance (Aug 20, 2024)
14-23470966-C-T		not specified	Uncertain significance (Dec 03, 2024)
14-23475177-A-G		not specified	Uncertain significance (Feb 23, 2023)
14-23475211-T-C		not specified	Uncertain significance (Aug 14, 2023)
14-23475275-T-A		not specified	Uncertain significance (Jun 19, 2024)
14-23475743-C-G		not specified	Uncertain significance (Aug 17, 2021)
14-23476064-A-T		not specified	Uncertain significance (Nov 10, 2024)
14-23476107-G-A		not specified	Uncertain significance (Sep 20, 2023)
14-23476143-G-A		not specified	Uncertain significance (Jun 18, 2024)
14-23476289-C-T		not specified	Uncertain significance (Jan 24, 2023)
14-23476355-C-T		not specified	Uncertain significance (Dec 03, 2024)
14-23476374-A-C		not specified	Uncertain significance (Jul 10, 2024)
14-23476374-A-G		not specified	Uncertain significance (Feb 14, 2023)
14-23476374-A-T		not specified	Uncertain significance (Sep 02, 2024)
14-23476383-G-A		not specified	Uncertain significance (Nov 15, 2024)
14-23476404-A-G		not specified	Uncertain significance (Feb 05, 2024)
14-23477207-T-C		not specified	Uncertain significance (Jan 23, 2023)
14-23477279-A-G		not specified	Uncertain significance (Oct 13, 2023)
14-23477311-C-A		not specified	Uncertain significance (Sep 21, 2023)
14-23477346-A-G		not specified	Uncertain significance (Aug 17, 2022)
14-23477524-C-T		not specified	Uncertain significance (May 18, 2023)
14-23477548-C-G		not specified	Uncertain significance (Feb 12, 2024)
14-23478013-G-A		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NGDN	protein_coding	protein_coding	ENST00000408901	11	40175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.04e-8	0.680	125632	0	115	125747	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0236	190	191	0.995	0.0000117	2053
Missense in Polyphen		43	52.42	0.82029		612
Synonymous	-0.395	63	59.1	1.07	0.00000265	597
Loss of Function	1.28	15	21.4	0.702	0.00000127	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000485	0.000485
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000669	0.000668
Middle Eastern	0.000109	0.000109
South Asian	0.000784	0.000784
Other	0.000326	0.000326

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

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

Mouse Genome Informatics

• Gene name: Ngdn

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