NM_153240.5(NPHP3):c.3027A>G (p.Lys1009=) AND Nephronophthisis

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 9, 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:: RCV003747732.1

Allele description

NM_153240.5(NPHP3):c.3027A>G (p.Lys1009=)

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.3027A>G (p.Lys1009=)

HGVS:

NC_000003.12:g.132688748T>C
NG_008130.2:g.38685A>G
NM_153240.5:c.3027A>GMANE SELECT
NP_694972.3:p.Lys1009=
NC_000003.11:g.132407592T>C
NR_037804.1:n.3033A>G

Molecular consequence:

NR_037804.1:n.3033A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_153240.5:c.3027A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Nephronophthisis
Synonyms:: juvenile nephronophthisis
Identifiers:: MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

Recent activity

Clear Turn Off Turn On

transcription elongation factor A protein-like 4 isoform 1 [Homo sapiens]
transcription elongation factor A protein-like 4 isoform 1 [Homo sapiens]
gi|65505873|ref|NP_079139.4|

Protein
Homologene neighbors for GEO Profiles (Select 122093208) (0)
GEO Profiles
Homologene neighbors for GEO Profiles (Select 122075444) (0)
GEO Profiles
Profile neighbors for GEO Profiles (Select 122082225) (199)
GEO Profiles
Profile neighbors for GEO Profiles (Select 122075443) (199)
GEO Profiles

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004454985	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Apr 9, 2023)	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

SCV004454985

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Apr 9, 2023)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004454985.1

#	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: Feb 28, 2024

ClinVar

Relating variation to medicine