NM_153240.5(NPHP3):c.70G>A (p.Gly24Ser) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 6, 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:: RCV003240370.2

Allele description [Variation Report for NM_153240.5(NPHP3):c.70G>A (p.Gly24Ser)]

NM_153240.5(NPHP3):c.70G>A (p.Gly24Ser)

Genes:

LOC129937586:ATAC-STARR-seq lymphoblastoid silent region 14743 [Gene]
NPHP3-AS1:NPHP3 antisense RNA 1 [Gene - HGNC]
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.70G>A (p.Gly24Ser)

HGVS:

NC_000003.12:g.132722286C>T
NG_008130.2:g.5147G>A
NG_170596.1:g.321C>T
NM_153240.5:c.70G>AMANE SELECT
NP_694972.3:p.Gly24Ser
NC_000003.11:g.132441130C>T
NM_153240.4:c.70G>A
NR_002811.2:n.537C>T
NR_037804.1:n.174G>A
NR_152743.1:n.537C>T

Protein change:

G24S

Molecular consequence:

NM_153240.5:c.70G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_002811.2:n.537C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_037804.1:n.174G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_152743.1:n.537C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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D4Dcr7 AND (alive[prop]) (1)
Gene
TRV_04922 [Trichophyton verrucosum HKI 0517]
TRV_04922 [Trichophyton verrucosum HKI 0517]
Gene ID:9577827

Gene
RecName: Full=Testis-specific gene 13 protein
RecName: Full=Testis-specific gene 13 protein
gi|81881664|sp|Q9DA17.1|TSG13_MOUSE

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003941617	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 6, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003941617

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 6, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV003941617.2

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

Description

The c.70G>A (p.G24S) alteration is located in exon 1 (coding exon 1) of the NPHP3 gene. This alteration results from a G to A substitution at nucleotide position 70, causing the glycine (G) at amino acid position 24 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	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: Sep 1, 2024

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