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NM_001128178.3(NPHP1):c.625-1G>A AND Nephronophthisis 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 23, 2023
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:
RCV003153060.1

Allele description [Variation Report for NM_001128178.3(NPHP1):c.625-1G>A]

NM_001128178.3(NPHP1):c.625-1G>A

Gene:
NPHP1:nephrocystin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q13
Genomic location:
Preferred name:
NM_001128178.3(NPHP1):c.625-1G>A
HGVS:
  • NC_000002.12:g.110165156C>T
  • NG_008287.1:g.44907G>A
  • NM_000272.5:c.625-1G>A
  • NM_001128178.3:c.625-1G>AMANE SELECT
  • NM_001128179.3:c.439-1G>A
  • NM_001374256.1:c.625-1G>A
  • NM_001374257.1:c.625-1G>A
  • NM_207181.4:c.625-1G>A
  • NC_000002.11:g.110922733C>T
Molecular consequence:
  • NM_000272.5:c.625-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001128178.3:c.625-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001128179.3:c.439-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374256.1:c.625-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001374257.1:c.625-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_207181.4:c.625-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0038418043billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Feb 23, 2023) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 3billion, SCV003841804.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 10, 2023