NM_153240.5(NPHP3):c.2694-2_2694-1del AND multiple conditions

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 19, 2025
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002500658.7

Allele description [Variation Report for NM_153240.5(NPHP3):c.2694-2_2694-1del]

NM_153240.5(NPHP3):c.2694-2_2694-1del

Genes:

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

Variant type:

Deletion

Cytogenetic location:

3q22.1

Genomic location:

Preferred name:

NM_153240.5(NPHP3):c.2694-2_2694-1del

Other names:

splice site

HGVS:

NC_000003.12:g.132689264_132689265del
NG_008130.2:g.38168_38169del
NM_153240.5:c.2694-2_2694-1delMANE SELECT
NC_000003.11:g.132408108_132408109del
NG_008130.1:g.38168_38169del
NM_153240.4:c.2694-2_2694-1del
NM_153240.4:c.2694-2_2694-1delAG
NM_153240.5:c.2694-2_2694-1delAGMANE SELECT
c.2694-2_2694-1delAG

Links:

OMIM: 608002.0004; dbSNP: rs751527253

Molecular consequence:

NM_153240.5:c.2694-2_2694-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002810601	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 8, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005871551	Juno Genomics, Hangzhou Juno Genomics, Inc	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV007580611	First Genomix Gene Laboratory, Genetic Diagnostics Department	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 19, 2025)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002810601

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 8, 2024)

germline

clinical testing

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

SCV005871551

Juno Genomics, Hangzhou Juno Genomics, Inc

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

clinical testing

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

SCV007580611

First Genomix Gene Laboratory, Genetic Diagnostics Department

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 19, 2025)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002810601.2

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

#	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

From Juno Genomics, Hangzhou Juno Genomics, Inc, SCV005871551.2

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

Description

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;For recessive disorders, detected in trans with a pathogenic variant.;Patient's phenotype or family history is highly specific for a disease with a single genetic etiology.;Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.;Null variant in a gene where loss of function (LOF) is a known mechanism of disease.

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

From First Genomix Gene Laboratory, Genetic Diagnostics Department, SCV007580611.1

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

Description

As part of Carrier Screening testing performed at First Genomix, this variant was identified in a heterozygous state in a patient who is not affected with this condition.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jul 14, 2026

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