NM_004646.4(NPHS1):c.71T>A (p.Leu24Ter) AND Finnish congenital nephrotic syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 25, 2022
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:: RCV002307169.2

Allele description [Variation Report for NM_004646.4(NPHS1):c.71T>A (p.Leu24Ter)]

NM_004646.4(NPHS1):c.71T>A (p.Leu24Ter)

Genes:

NPHS1:NPHS1 adhesion molecule, nephrin [Gene - OMIM - HGNC]
KIRREL2:kirre like nephrin family adhesion molecule 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.12

Genomic location:

Preferred name:

NM_004646.4(NPHS1):c.71T>A (p.Leu24Ter)

HGVS:

NC_000019.10:g.35851660A>T
NG_013356.2:g.22628T>A
NG_051206.1:g.5026A>T
NM_004646.4:c.71T>AMANE SELECT
NP_004637.1:p.Leu24Ter
NP_004637.1:p.Leu24Ter
LRG_693t1:c.71T>A
LRG_693:g.22628T>A
LRG_693p1:p.Leu24Ter
NC_000019.9:g.36342562A>T
NM_004646.3:c.71T>A

Protein change:

L24*

Molecular consequence:

NM_004646.4:c.71T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Finnish congenital nephrotic syndrome (NPHS1)
Synonyms:: NEPHROTIC SYNDROME, TYPE 1; Nephrosis 1, congenital, Finnish type; Congenital nephrotic syndrome 1
Identifiers:: MONDO: MONDO:0009732; MedGen: C0403399; Orphanet: 839; OMIM: 256300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002604640	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Feb 25, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002604640

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Feb 25, 2022)

unknown

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

Details of each submission

From Myriad Genetics, Inc., SCV002604640.2

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

Description

NM_004646.3(NPHS1):c.71T>A(L24*) is expected to be pathogenic in the context of nephrotic syndrome, NPHS1-related. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in NPHS1, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

#	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

Last Updated: Dec 24, 2022

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