NPNT

nephronectin

Basic information

Region (hg38): 4:105894774-106004027

Links

ENSG00000168743 ∙ NCBI:255743 ∙ OMIM:610306 ∙ HGNC:27405 ∙ Uniprot:Q6UXI9 ∙ 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 NPNT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPNT 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				2		2
missense			36	6		42
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	8	0

Variants in NPNT

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

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

Position	Type	Phenotype	Significance	ClinVar
4-105895659-T-G		not specified	Uncertain significance (Nov 14, 2023)
4-105895680-G-A		not specified	Uncertain significance (May 26, 2022)
4-105895711-A-C		not specified	Uncertain significance (Jul 25, 2023)
4-105895711-A-G		not specified	Uncertain significance (Dec 27, 2022)
4-105895717-A-T		not specified	Uncertain significance (Oct 10, 2023)
4-105897902-T-G		not specified	Uncertain significance (Apr 06, 2024)
4-105897932-C-T			Likely benign (Feb 01, 2023)
4-105897938-C-T		not specified	Uncertain significance (Apr 20, 2023)
4-105897939-G-A		not specified	Uncertain significance (Jul 14, 2023)
4-105897954-T-C		not specified	Uncertain significance (May 18, 2022)
4-105897978-G-A		not specified	Uncertain significance (Dec 14, 2023)
4-105927417-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-105937013-A-C			Likely benign (Mar 01, 2023)
4-105938318-A-G		not specified	Uncertain significance (May 04, 2022)
4-105938337-G-T		not specified	Uncertain significance (Apr 23, 2024)
4-105938382-C-T			Likely benign (Mar 01, 2023)
4-105938384-G-A		not specified	Uncertain significance (Feb 15, 2023)
4-105940089-G-A		not specified	Uncertain significance (Dec 16, 2023)
4-105940111-C-T		not specified	Uncertain significance (Jun 11, 2024)
4-105940159-G-A		not specified	Uncertain significance (Jan 03, 2022)
4-105940173-G-A		not specified	Uncertain significance (Dec 07, 2021)
4-105940181-G-A		not specified	Uncertain significance (Jan 23, 2023)
4-105940562-G-A		not specified	Uncertain significance (Sep 30, 2021)
4-105940571-A-G		not specified	Uncertain significance (Feb 26, 2024)
4-105940587-C-G			Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPNT	protein_coding	protein_coding	ENST00000427316	13	109253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-10	0.896	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0940	341	336	1.01	0.0000175	3851
Missense in Polyphen		116	132.97	0.87237		1581
Synonymous	0.610	111	119	0.929	0.00000638	1168
Loss of Function	1.85	20	31.1	0.642	0.00000156	368

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000440	0.000435
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000252	0.000246
Middle Eastern	0.000440	0.000435
South Asian	0.000171	0.000163
Other	0.000343	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functional ligand of integrin alpha-8/beta-1 in kidney development. Regulates the expression of GDNF with integrin alpha- 8/beta-1 which is essential for kidney development. May also play a role in the development and function of various tissues, regulating cell adhesion, spreading and survival through the binding of several integrins (By similarity). {ECO:0000250}.
• Pathway: Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.124
• rvis_EVS: 1.8
• rvis_percentile_EVS: 96.93

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.267
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.419

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npnt
• Phenotype: renal/urinary system phenotype

Zebrafish Information Network

• Gene name: npnt
• Affected structure: atrioventricular valve
• Phenotype tag: abnormal
• Phenotype quality: increased length

Gene ontology

• Biological process: ureteric bud development;branching involved in ureteric bud morphogenesis;cell-matrix adhesion;positive regulation of alkaline phosphatase activity;positive regulation of cell-substrate adhesion;extracellular matrix organization;positive regulation of transforming growth factor beta receptor signaling pathway;cell-cell adhesion mediated by integrin;establishment of protein localization;positive regulation of osteoblast differentiation;positive regulation of smooth muscle contraction;positive regulation of ERK1 and ERK2 cascade;cellular response to tumor necrosis factor;pilomotor reflex;positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation
• Cellular component: extracellular region;basement membrane;smooth muscle contractile fiber;integrin alpha8-beta1 complex;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: integrin binding;extracellular matrix structural constituent;calcium ion binding