NM_153240.5(NPHP3):c.3504A>G (p.Ala1168=) AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Mar 5, 2024
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:: RCV005036040.1

Allele description [Variation Report for NM_153240.5(NPHP3):c.3504A>G (p.Ala1168=)]

NM_153240.5(NPHP3):c.3504A>G (p.Ala1168=)

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.3504A>G (p.Ala1168=)

HGVS:

NC_000003.12:g.132684620T>C
NG_008130.2:g.42813A>G
NM_153240.5:c.3504A>GMANE SELECT
NP_694972.3:p.Ala1168=
NC_000003.11:g.132403464T>C
NG_008130.1:g.42813A>G
NM_153240.4:c.3504A>G
NR_037804.1:n.3510A>G

Links:

dbSNP: rs371505908

Molecular consequence:

NR_037804.1:n.3510A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_153240.5:c.3504A>G - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005663542	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Mar 5, 2024)	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

SCV005663542

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Mar 5, 2024)

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	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, SCV005663542.1

#	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

Last Updated: Jun 20, 2026

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