NPHP3-AS1

NPHP3 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 3:132721750-132895230

Previous symbols: [ "NCRNA00119" ]

Links

ENSG00000248724 ∙ NCBI:348808 ∙ ∙ HGNC:24129 ∙ ∙ ∙ 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 NPHP3-AS1 gene.

• Nephronophthisis (106 variants)
• not provided (43 variants)
• Renal-hepatic-pancreatic dysplasia 1 (13 variants)
• Nephronophthisis 3 (11 variants)
• not specified (10 variants)
• NPHP3-related Meckel-like syndrome (9 variants)
• Renal-hepatic-pancreatic dysplasia 1;Nephronophthisis 3;NPHP3-related Meckel-like syndrome (7 variants)
• Renal-hepatic-pancreatic dysplasia 1;NPHP3-related Meckel-like syndrome;Nephronophthisis 3 (6 variants)
• Inborn genetic diseases (5 variants)
• Nephronophthisis 3;NPHP3-related Meckel-like syndrome;Renal-hepatic-pancreatic dysplasia 1 (5 variants)
• Kidney disorder (3 variants)
• Meckel-Gruber syndrome (3 variants)
• Nephronophthisis 3;Renal-hepatic-pancreatic dysplasia 1;NPHP3-related Meckel-like syndrome (2 variants)
• Joubert syndrome and related disorders (2 variants)
• NPHP3-related Meckel-like syndrome;Nephronophthisis 3;Renal-hepatic-pancreatic dysplasia 1 (2 variants)
• NPHP3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPHP3-AS1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	7	4	76	43	5	135
Total	7	4	76	43	5

Highest pathogenic variant AF is 0.0000132

Variants in NPHP3-AS1

This is a list of pathogenic ClinVar variants found in the NPHP3-AS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-132721763-C-A			Likely benign (Sep 11, 2018)
3-132721836-G-A			Likely benign (Jul 15, 2018)
3-132721943-G-C		Nephronophthisis	Likely benign (Nov 20, 2023)
3-132721944-C-T		Nephronophthisis	Likely benign (Aug 26, 2022)
3-132721945-G-A		not specified • Nephronophthisis • Renal-hepatic-pancreatic dysplasia 1;Nephronophthisis 3;NPHP3-related Meckel-like syndrome	Likely benign (Dec 19, 2023)
3-132721947-C-A		Nephronophthisis	Likely benign (Oct 17, 2023)
3-132721954-CG-C		NPHP3-related disorder	Likely benign (Jun 08, 2022)
3-132721956-G-A		Nephronophthisis	Likely benign (Oct 27, 2023)
3-132721956-G-C			Uncertain significance (Nov 23, 2015)
3-132721962-C-G		Nephronophthisis	Likely pathogenic (Sep 04, 2021)
3-132721963-C-G		Nephronophthisis	Uncertain significance (Aug 23, 2022)
3-132721964-T-C		Nephronophthisis	Uncertain significance (Aug 12, 2022)
3-132721965-G-A		Nephronophthisis	Pathogenic (Apr 08, 2022)
3-132721967-A-T		Nephronophthisis	Uncertain significance (Aug 26, 2021)
3-132721972-G-C		NPHP3-related Meckel-like syndrome • Nephronophthisis 3 • Renal-hepatic-pancreatic dysplasia 1 • Nephronophthisis	Conflicting classifications of pathogenicity (Nov 19, 2023)
3-132721979-AGCCGC-A		Nephronophthisis 3	Pathogenic (Feb 01, 2020)
3-132721983-G-A		Nephronophthisis	Uncertain significance (Nov 01, 2021)
3-132721986-T-C			Uncertain significance (Jan 18, 2017)
3-132721989-T-A		Nephronophthisis	Uncertain significance (Aug 14, 2023)
3-132721994-G-C		Nephronophthisis	Uncertain significance (Aug 21, 2019)
3-132721995-T-G		Nephronophthisis 3	Uncertain significance (Aug 01, 2021)
3-132721997-T-A		Nephronophthisis	Uncertain significance (Feb 15, 2022)
3-132722002-C-T		Nephronophthisis	Likely benign (Sep 12, 2023)
3-132722003-T-C		Nephronophthisis	Uncertain significance (Nov 13, 2023)
3-132722009-T-C		Nephronophthisis	Uncertain significance (Mar 18, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP