NPDC1

neural proliferation, differentiation and control 1

Basic information

Region (hg38): 9:137039463-137046179

Links

ENSG00000107281 ∙ NCBI:56654 ∙ OMIM:605798 ∙ HGNC:7899 ∙ Uniprot:Q9NQX5 ∙ 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 NPDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPDC1 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			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	0

Variants in NPDC1

This is a list of pathogenic ClinVar variants found in the NPDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137040382-G-A		not specified	Uncertain significance (Sep 01, 2021)
9-137040408-G-A		not specified	Uncertain significance (Oct 25, 2023)
9-137040414-T-G		not specified	Uncertain significance (Nov 20, 2024)
9-137040423-C-T		not specified	Uncertain significance (Jul 10, 2023)
9-137040522-G-A		not specified	Uncertain significance (Mar 20, 2024)
9-137040533-G-T		not specified	Uncertain significance (Nov 11, 2024)
9-137040558-C-T		not specified	Uncertain significance (May 23, 2023)
9-137040579-G-C		not specified	Uncertain significance (May 04, 2023)
9-137040684-G-T		not specified	Uncertain significance (Jul 02, 2024)
9-137040686-G-T		not specified	Uncertain significance (Aug 05, 2024)
9-137040702-C-T		not specified	Uncertain significance (Feb 07, 2023)
9-137040717-C-A		not specified	Uncertain significance (Mar 01, 2025)
9-137040721-G-C		not specified	Uncertain significance (Sep 17, 2021)
9-137040820-C-T		not specified	Uncertain significance (Dec 17, 2021)
9-137040843-C-T		not specified	Uncertain significance (Oct 25, 2022)
9-137040865-G-A		not specified	Uncertain significance (Jun 26, 2024)
9-137040870-G-A		not specified	Uncertain significance (Jun 04, 2024)
9-137040871-G-C		not specified	Uncertain significance (Mar 04, 2024)
9-137040894-A-G		not specified	Uncertain significance (Apr 10, 2023)
9-137040895-G-C		not specified	Uncertain significance (Jun 13, 2023)
9-137040900-G-C		not specified	Uncertain significance (Dec 05, 2022)
9-137040907-G-A		not specified	Uncertain significance (Mar 16, 2022)
9-137040963-C-A		not specified	Uncertain significance (Dec 10, 2024)
9-137040963-C-T		not specified	Uncertain significance (Jan 20, 2025)
9-137040969-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPDC1	protein_coding	protein_coding	ENST00000371601	9	6734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0296	0.961	125028	0	4	125032	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00348	187	187	1.00	0.0000130	1988
Missense in Polyphen		71	82.932	0.85612		817
Synonymous	-1.31	99	83.7	1.18	0.00000606	736
Loss of Function	2.28	5	14.3	0.350	6.77e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000893	0.0000893
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000106	0.00000888
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Suppresses oncogenic transformation in neural and non- neural cells and down-regulates neural cell proliferation. Might be involved in transcriptional regulation (By similarity). {ECO:0000250}.
• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.109
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.778
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.467

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npdc1
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding