NM_015102.5(NPHP4):c.1788_1791del (p.Ser597fs) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 18, 2016
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:: RCV000490323.1

Allele description [Variation Report for NM_015102.5(NPHP4):c.1788_1791del (p.Ser597fs)]

NM_015102.5(NPHP4):c.1788_1791del (p.Ser597fs)

Gene:

NPHP4:nephrocystin 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p36.31

Genomic location:

Preferred name:

NM_015102.5(NPHP4):c.1788_1791del (p.Ser597fs)

HGVS:

NC_000001.11:g.5905457_5905460del
NG_011724.2:g.92013_92016del
NM_001291593.2:c.249_252del
NM_001291594.2:c.252_255del
NM_015102.5:c.1788_1791delMANE SELECT
NP_001278522.1:p.Ser84fs
NP_001278523.1:p.Ser85fs
NP_055917.1:p.Ser597fs
NC_000001.10:g.5965517_5965520del
NM_001291593.1:c.249_252delCTCC
NR_111987.2:n.2005_2008del

Protein change:

S597fs

Links:

dbSNP: rs747699128

NCBI 1000 Genomes Browser:

rs747699128

Molecular consequence:

NM_001291593.2:c.249_252del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291594.2:c.252_255del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015102.5:c.1788_1791del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_111987.2:n.2005_2008del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Nephronophthisis 4 (NPHP4)
Synonyms:: NEPHRONOPHTHISIS 4, JUVENILE
Identifiers:: MONDO: MONDO:0011752; MedGen: C1847013; Orphanet: 655; OMIM: 606966

Name:: Senior-Loken syndrome 4 (SLSN4)
Identifiers:: MONDO: MONDO:0011756; MedGen: C1846979; Orphanet: 3156; OMIM: 606996

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267421	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 12205563, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267421

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2016)

germline

reference population

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution.

Otto E, Hoefele J, Ruf R, Mueller AM, Hiller KS, Wolf MT, Schuermann MJ, Becker A, Birkenhäger R, Sudbrak R, Hennies HC, Nürnberg P, Hildebrandt F.

Am J Hum Genet. 2002 Nov;71(5):1161-7. Epub 2002 Aug 29.

PubMed [citation]

PMID:: 12205563
PMCID:: PMC385091

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267421.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (2)

#	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		1	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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