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NM_153240.5(NPHP3):c.3399C>T (p.Asp1133=) AND multiple conditions

Germline classification:
Likely benign (1 submission)
Last evaluated:
Sep 17, 2021
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:
RCV002486912.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.3399C>T (p.Asp1133=)]

NM_153240.5(NPHP3):c.3399C>T (p.Asp1133=)

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.3399C>T (p.Asp1133=)
HGVS:
  • NC_000003.12:g.132684725G>A
  • NG_008130.2:g.42708C>T
  • NM_153240.5:c.3399C>TMANE SELECT
  • NP_694972.3:p.Asp1133=
  • NC_000003.11:g.132403569G>A
  • NM_153240.4:c.3399C>T
  • NR_037804.1:n.3405C>T
Links:
dbSNP: rs766231228
NCBI 1000 Genomes Browser:
rs766231228
Molecular consequence:
  • NR_037804.1:n.3405C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_153240.5:c.3399C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Renal-hepatic-pancreatic dysplasia 1 (RHPD1)
Identifiers:
MONDO: MONDO:0008833; MedGen: C3715199; OMIM: 208540
Name:
Nephronophthisis 3 (NPHP3)
Synonyms:
Adolescent nephronophthisis
Identifiers:
MONDO: MONDO:0011456; MedGen: C1858392; Orphanet: 655; OMIM: 604387
Name:
NPHP3-related Meckel-like syndrome
Synonyms:
GOLDSTON SYNDROME; Meckel syndrome type 7
Identifiers:
MONDO: MONDO:0009966; MedGen: C2673885; Orphanet: 3032; OMIM: 267010

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002795009Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Sep 17, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot 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 Fulgent Genetics, Fulgent Genetics, SCV002795009.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 16, 2025