NM_153240.5(NPHP3):c.1706C>G (p.Ser569Ter) AND Nephronophthisis

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 21, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003043960.2

Allele description

NM_153240.5(NPHP3):c.1706C>G (p.Ser569Ter)

Genes:

NPHP3-ACAD11:NPHP3-ACAD11 readthrough (NMD candidate) [Gene - HGNC]
NPHP3:nephrocystin 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q22.1

Genomic location:

Preferred name:

NM_153240.5(NPHP3):c.1706C>G (p.Ser569Ter)

HGVS:

NC_000003.12:g.132700371G>C
NG_008130.2:g.27062C>G
NM_153240.5:c.1706C>GMANE SELECT
NP_694972.3:p.Ser569Ter
NC_000003.11:g.132419215G>C
NR_037804.1:n.1810C>G

Protein change:

S569*

Molecular consequence:

NR_037804.1:n.1810C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_153240.5:c.1706C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Nephronophthisis
Synonyms:: juvenile nephronophthisis
Identifiers:: MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

Recent activity

Clear Turn Off Turn On

Chromosome neighbors for GEO Profiles (Select 11780251) (20)
GEO Profiles
KLK2 kallikrein related peptidase 2 [Homo sapiens]
KLK2 kallikrein related peptidase 2 [Homo sapiens]
Gene ID:3817

Gene
Gene Links for GEO Profiles (Select 109707125) (1)
Gene
APMAP adipocyte plasma membrane associated protein [Homo sapiens]
APMAP adipocyte plasma membrane associated protein [Homo sapiens]
Gene ID:57136

Gene
Gene Links for GEO Profiles (Select 45802583) (1)
Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003338555	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 21, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18371931, 23559409, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003338555

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 21, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.

Bergmann C, Fliegauf M, Brüchle NO, Frank V, Olbrich H, Kirschner J, Schermer B, Schmedding I, Kispert A, Kränzlin B, Nürnberg G, Becker C, Grimm T, Girschick G, Lynch SA, Kelehan P, Senderek J, Neuhaus TJ, Stallmach T, Zentgraf H, Nürnberg P, Gretz N, et al.

Am J Hum Genet. 2008 Apr;82(4):959-70. doi: 10.1016/j.ajhg.2008.02.017. Epub 2008 Mar 27.

PubMed [citation]

PMID:: 18371931
PMCID:: PMC2427297

Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy.

Halbritter J, Porath JD, Diaz KA, Braun DA, Kohl S, Chaki M, Allen SJ, Soliman NA, Hildebrandt F, Otto EA; GPN Study Group..

Hum Genet. 2013 Aug;132(8):865-84. doi: 10.1007/s00439-013-1297-0. Epub 2013 Apr 5.

PubMed [citation]

PMID:: 23559409
PMCID:: PMC4643834

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003338555.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser569*) in the NPHP3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

ClinVar

Relating variation to medicine