NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr) AND Renal-hepatic-pancreatic dysplasia 1

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 28, 2019
Review status:: criteria provided, conflicting classifications

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:: RCV000987337.15

Allele description [Variation Report for NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr)]

NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr)

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.154G>A (p.Ala52Thr)

HGVS:

NC_000003.12:g.132722202C>T
NG_008130.2:g.5231G>A
NM_153240.5:c.154G>AMANE SELECT
NP_694972.3:p.Ala52Thr
NC_000003.11:g.132441046C>T
NG_008130.1:g.5231G>A
NM_153240.4:c.154G>A
NR_002811.2:n.453C>T
NR_037804.1:n.258G>A
NR_152743.1:n.453C>T

Protein change:

A52T

Links:

dbSNP: rs145643112

NCBI 1000 Genomes Browser:

rs145643112

Molecular consequence:

NM_153240.5:c.154G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_002811.2:n.453C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_037804.1:n.258G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_152743.1:n.453C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Renal-hepatic-pancreatic dysplasia 1 (RHPD1)
Identifiers:: MONDO: MONDO:0008833; MedGen: C3715199; OMIM: 208540

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001136605	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001308213	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001136605

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV001308213

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	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

Details of each submission

From Mendelics, SCV001136605.1

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

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

From Illumina Laboratory Services, Illumina, SCV001308213.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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: May 7, 2024

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