NM_000272.3(NPHP1):c.625-3dup AND multiple conditions

Germline classification:: Uncertain significance (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:: RCV000490473.1

Allele description [Variation Report for NM_000272.3(NPHP1):c.625-3dup]

NM_000272.3(NPHP1):c.625-3dup

Gene:

NPHP1:nephrocystin 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

2q13

Genomic location:

Preferred name:

NM_000272.3(NPHP1):c.625-3dup

HGVS:

NC_000002.12:g.110165163dup
NG_008287.1:g.44905dup
NM_000272.5:c.625-3dup
NM_001128178.3:c.625-3dupMANE SELECT
NM_001128179.3:c.439-3dup
NM_001374256.1:c.625-3dup
NM_001374257.1:c.625-3dup
NM_207181.4:c.625-3dup
NC_000002.11:g.110922734_110922735insA
NC_000002.11:g.110922740dup
NM_000272.3:c.625-3dupT

Links:

dbSNP: rs200118387

NCBI 1000 Genomes Browser:

rs200118387

Molecular consequence:

NM_000272.5:c.625-3dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001128178.3:c.625-3dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001128179.3:c.439-3dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001374256.1:c.625-3dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001374257.1:c.625-3dup - intron variant - [Sequence Ontology: SO:0001627]
NM_207181.4:c.625-3dup - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Joubert syndrome with renal defect
Synonyms:: Joubert syndrome with renal anomalies; Joubert syndrome 4
Identifiers:: MONDO: MONDO:0012308; MedGen: C1846790; Orphanet: 220497; OMIM: 609583

Name:: Nephronophthisis 1 (NPHP1)
Synonyms:: Nephronophthisis familial juvenile
Identifiers:: MONDO: MONDO:0009728; MedGen: C1855681; Orphanet: 655; OMIM: 256100

Name:: Senior-Loken syndrome 1 (SLSN1)
Synonyms:: Juvenile nephronophthisis with Leber amaurosis
Identifiers:: MONDO: MONDO:0009962; MedGen: C4551559; Orphanet: 3156; OMIM: 266900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267420	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 18, 2016)	germline	reference population	PubMed (3) [See all records that cite these PMIDs] 15138899, 10839884, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267420

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 18, 2016)

germline

reference population

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
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

The NPHP1 gene deletion associated with juvenile nephronophthisis is present in a subset of individuals with Joubert syndrome.

Parisi MA, Bennett CL, Eckert ML, Dobyns WB, Gleeson JG, Shaw DW, McDonald R, Eddy A, Chance PF, Glass IA.

Am J Hum Genet. 2004 Jul;75(1):82-91. Epub 2004 May 11.

PubMed [citation]

PMID:: 15138899
PMCID:: PMC1182011

Children with ocular motor apraxia type Cogan carry deletions in the gene (NPHP1) for juvenile nephronophthisis.

Betz R, Rensing C, Otto E, Mincheva A, Zehnder D, Lichter P, Hildebrandt F.

J Pediatr. 2000 Jun;136(6):828-31.

PubMed [citation]

PMID:: 10839884

See all PubMed Citations (3)

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267420.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (3)

#	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: Nov 10, 2024

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