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NPHP3-ACAD11

NPHP3-ACAD11 readthrough (NMD candidate)

Basic information

Region (hg38): 3:132558141-132722459

Links

ENSG00000274810 ∙ NCBI:100532724 ∙ ∙ HGNC:48351 ∙ ∙ ∙ 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-ACAD11 gene.

  • Nephronophthisis (818 variants)
  • not provided (490 variants)
  • Nephronophthisis 3 (115 variants)
  • Renal-hepatic-pancreatic dysplasia 1 (112 variants)
  • NPHP3-related Meckel-like syndrome (97 variants)
  • Inborn genetic diseases (95 variants)
  • not specified (62 variants)
  • Renal-hepatic-pancreatic dysplasia 1;Nephronophthisis 3;NPHP3-related Meckel-like syndrome (50 variants)
  • Nephronophthisis 3;NPHP3-related Meckel-like syndrome;Renal-hepatic-pancreatic dysplasia 1 (36 variants)
  • Developmental and epileptic encephalopathy, 44 (25 variants)
  • Renal-hepatic-pancreatic dysplasia 1;NPHP3-related Meckel-like syndrome;Nephronophthisis 3 (21 variants)
  • Kidney disorder (19 variants)
  • NPHP3-related Meckel-like syndrome;Renal-hepatic-pancreatic dysplasia 1;Nephronophthisis 3 (19 variants)
  • NPHP3-related condition (15 variants)
  • Meckel-Gruber syndrome (14 variants)
  • Nephronophthisis 3;Renal-hepatic-pancreatic dysplasia 1;NPHP3-related Meckel-like syndrome (13 variants)
  • NPHP3-related Meckel-like syndrome;Nephronophthisis 3;Renal-hepatic-pancreatic dysplasia 1 (13 variants)
  • Joubert syndrome and related disorders (8 variants)
  • Spinocerebellar ataxia, autosomal recessive 24 (3 variants)
  • NPHP3-related disorders (3 variants)
  • UBA5-related condition (3 variants)
  • Fibrotic kidney disease (2 variants)
  • Developmental and epileptic encephalopathy, 44;Spinocerebellar ataxia, autosomal recessive 24 (2 variants)
  • Enlarged kidney;Multiple renal cysts;Anhydramnios (2 variants)
  • Early infantile epileptic encephalopathy with suppression bursts (1 variants)
  • Focal segmental glomerulosclerosis (1 variants)
  • Bardet-Biedl syndrome (1 variants)
  • See cases (1 variants)
  • Polycystic kidney dysplasia (1 variants)
  • Leber congenital amaurosis (1 variants)
  • UBA5-Related Disorders (1 variants)
  • - (1 variants)
  • Atypical hemolytic-uremic syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPHP3-ACAD11 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
clinvar
20
clinvar
1
clinvar
 23
missense
1
clinvar
68
clinvar
8
clinvar
1
clinvar
 78
nonsense
4
clinvar
3
clinvar
1
clinvar
 8
start loss
0
frameshift
4
clinvar
3
clinvar
1
clinvar
 8
inframe indel
1
clinvar
4
clinvar
 5
splice donor/acceptor (+/-2bp)
7
clinvar
12
clinvar
50
clinvar
34
clinvar
5
clinvar
 108
splice region
?
    Intron variants in splice region, excluding donor/acceptor (+/-2bp)
 0
non coding
?
    UTR, intron and other, non coding variants
68
clinvar
40
clinvar
535
clinvar
366
clinvar
63
clinvar
 1072
Total 83 60 661 428 70

Highest pathogenic variant AF is 0.00244

Variants in NPHP3-ACAD11

This is a list of pathogenic ClinVar variants found in the NPHP3-ACAD11 region.

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

Position Type Phenotype Significance ClinVar
3-132559003-C-T not specified Uncertain significance (Jul 27, 2022)2303773
3-132559005-C-T not specified Likely benign (Mar 02, 2023)2492970
3-132559012-C-G not specified Uncertain significance (Jul 14, 2022)2400029
3-132559021-C-T not specified Uncertain significance (Nov 10, 2022)2214874
3-132559062-C-T not specified Uncertain significance (Nov 16, 2021)2219602
3-132561139-T-C not specified Uncertain significance (Apr 05, 2023)2533257
3-132561166-G-A not specified Uncertain significance (Nov 18, 2022)2257074
3-132561170-C-A not specified Uncertain significance (Feb 05, 2024)3134559
3-132561184-T-C not specified Uncertain significance (Apr 20, 2023)2539194
3-132561187-G-A not specified Uncertain significance (Aug 01, 2022)2396808
3-132575844-C-T Likely benign (Mar 01, 2022)2654160
3-132575894-G-A not specified Uncertain significance (May 25, 2022)2363201
3-132576970-C-T not specified Uncertain significance (Dec 09, 2023)3134548
3-132578881-T-C not specified Likely benign (Jan 03, 2024)3134545
3-132579514-T-C not specified Uncertain significance (Aug 02, 2023)2615163
3-132579534-A-G not specified Uncertain significance (Dec 16, 2023)3134534
3-132579544-T-G not specified Uncertain significance (Nov 17, 2022)2326446
3-132601200-T-C not specified Uncertain significance (Aug 13, 2021)2245263
3-132601238-A-G not specified Uncertain significance (Sep 17, 2021)2226977
3-132601239-T-C not specified Uncertain significance (Jun 18, 2021)2233337
3-132601286-T-C not specified Uncertain significance (Jul 06, 2021)2235360
3-132603242-T-A not specified Uncertain significance (Oct 29, 2021)2396651
3-132603303-G-A not specified Uncertain significance (May 05, 2023)2544517
3-132605177-C-T Uncertain significance (Nov 11, 2013)166629
3-132618681-G-C not specified Uncertain significance (Dec 26, 2023)3134522

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Pathway
Wnt Signaling in Kidney Disease (Consensus)

Gene ontology

Biological process
Cellular component
kinesin complex
Molecular function
microtubule motor activity