NM_004646.4(NPHS1):c.14C>T (p.Thr5Met) AND Finnish congenital nephrotic syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 19, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001391132.4

Allele description [Variation Report for NM_004646.4(NPHS1):c.14C>T (p.Thr5Met)]

NM_004646.4(NPHS1):c.14C>T (p.Thr5Met)

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.14C>T (p.Thr5Met)

HGVS:

NC_000019.10:g.35851824G>A
NG_013356.2:g.22464C>T
NG_051206.1:g.5190G>A
NM_004646.4:c.14C>TMANE SELECT
NP_004637.1:p.Thr5Met
NP_004637.1:p.Thr5Met
LRG_693t1:c.14C>T
LRG_693:g.22464C>T
LRG_693p1:p.Thr5Met
NC_000019.9:g.36342726G>A
NM_004646.3:c.14C>T

Protein change:

T5M

Links:

dbSNP: rs191850409

NCBI 1000 Genomes Browser:

rs191850409

Molecular consequence:

NM_004646.4:c.14C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001593090	Precision Medicine Center, Zhengzhou University	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	research	PubMed (1) [See all records that cite this PMID]
SCV002060064	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Uncertain significance (Oct 19, 2021)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28476686, 31216994, 18436095 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001593090

Precision Medicine Center, Zhengzhou University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV002060064

Myriad Genetics, Inc.

criteria provided, single submitter

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

Uncertain significance
(Oct 19, 2021)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Mutation spectrum of genes associated with steroid-resistant nephrotic syndrome in Chinese children.

Wang Y, Dang X, He Q, Zhen Y, He X, Yi Z, Zhu K.

Gene. 2017 Aug 20;625:15-20. doi: 10.1016/j.gene.2017.04.050. Epub 2017 May 2.

PubMed [citation]

PMID:: 28476686

See all PubMed Citations (4)

Details of each submission

From Precision Medicine Center, Zhengzhou University, SCV001593090.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

Description

BP4:Multiple lines of computational evidence suggest no impact

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

From Myriad Genetics, Inc., SCV002060064.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

NM_004646.3(NPHS1):c.14C>T(T5M) is a missense variant classified as a variant of uncertain significance in the context of nephrotic syndrome, NPHS1-related. T5M has been observed in cases with relevant disease (PMID: 18436095, 28476686, 31216994). Functional assessments of this variant are not available in the literature. T5M has been observed in population frequency databases (gnomAD: EAS 0.32%). In summary, there is insufficient evidence to classify NM_004646.3(NPHS1):c.14C>T(T5M) as pathogenic or benign. 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: Sep 29, 2024

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