NDC1

NDC1 transmembrane nucleoporin, the group of Nucleoporins

Basic information

Region (hg38): 1:53765478-53838463

Previous symbols: [ "TMEM48" ]

Links

ENSG00000058804 ∙ NCBI:55706 ∙ OMIM:610115 ∙ HGNC:25525 ∙ Uniprot:Q9BTX1 ∙ 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 NDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDC1 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			38	3		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	3	0

Variants in NDC1

This is a list of pathogenic ClinVar variants found in the NDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-53772359-C-T		not specified	Uncertain significance (Dec 04, 2023)
1-53772372-T-C		not specified	Uncertain significance (Oct 25, 2022)
1-53772419-T-C		not specified	Uncertain significance (Dec 06, 2022)
1-53772420-C-T		not specified	Uncertain significance (Apr 23, 2024)
1-53772422-A-T		not specified	Uncertain significance (Sep 17, 2021)
1-53772441-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-53772486-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-53787201-G-A		not specified	Uncertain significance (Jul 30, 2024)
1-53787228-G-A		not specified	Uncertain significance (Oct 25, 2024)
1-53787250-G-C		not specified	Uncertain significance (Aug 10, 2024)
1-53789180-A-G		not specified	Uncertain significance (Apr 22, 2024)
1-53793238-A-C		not specified	Uncertain significance (Sep 11, 2024)
1-53793273-T-G		not specified	Uncertain significance (Nov 14, 2024)
1-53796745-T-C		not specified	Uncertain significance (Apr 17, 2023)
1-53796907-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-53796952-G-A		not specified	Uncertain significance (Aug 28, 2024)
1-53796959-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-53796961-T-C		not specified	Uncertain significance (Apr 12, 2022)
1-53797031-G-T		not specified	Uncertain significance (May 26, 2023)
1-53797052-A-G		not specified	Uncertain significance (Aug 12, 2021)
1-53797108-A-G		not specified	Uncertain significance (Aug 19, 2021)
1-53800716-T-A		not specified	Uncertain significance (Jan 09, 2024)
1-53800752-G-C		not specified	Uncertain significance (Sep 14, 2023)
1-53800792-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-53800809-C-T		Cleft palate;Retinal disorder;Global developmental delay	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDC1	protein_coding	protein_coding	ENST00000371429	18	73401

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000678	125733	0	11	125744	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	290	347	0.835	0.0000167	4366
Missense in Polyphen		88	122.79	0.7167		1680
Synonymous	-0.875	139	126	1.10	0.00000608	1309
Loss of Function	5.17	4	38.7	0.103	0.00000182	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000943	0.0000924
European (Non-Finnish)	0.0000627	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000747	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the nuclear pore complex (NPC), which plays a key role in de novo assembly and insertion of NPC in the nuclear envelope. Required for NPC and nuclear envelope assembly, possibly by forming a link between the nuclear envelope membrane and soluble nucleoporins, thereby anchoring the NPC in the membrane. {ECO:0000269|PubMed:16600873, ECO:0000269|PubMed:16702233}.
• Pathway: RNA transport - Homo sapiens (human);tRNA processing;Disease;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Infectious disease;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;SUMOylation;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;Nuclear Pore Complex (NPC) Disassembly;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Interactions of Vpr with host cellular proteins;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.857
• hipred: Y
• hipred_score: 0.590
• ghis: 0.649

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndc1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; reproductive system phenotype; limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Biological process: mRNA export from nucleus;nuclear pore organization;synapsis;spermatogenesis;protein transport;viral process;nuclear pore distribution;nuclear pore complex assembly
• Cellular component: nuclear envelope;nuclear pore;cytoplasm;plasma membrane;actin cytoskeleton;membrane;integral component of membrane;nuclear membrane;nuclear pore transmembrane ring
• Molecular function: structural constituent of nuclear pore