NM_022098.4(XPNPEP3):c.645del (p.Ser216fs) AND Nephronophthisis-like nephropathy 1

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Feb 11, 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:: RCV001310284.3

Allele description [Variation Report for NM_022098.4(XPNPEP3):c.645del (p.Ser216fs)]

NM_022098.4(XPNPEP3):c.645del (p.Ser216fs)

Gene:

XPNPEP3:X-prolyl aminopeptidase 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q13.2

Genomic location:

Preferred name:

NM_022098.4(XPNPEP3):c.645del (p.Ser216fs)

HGVS:

NC_000022.11:g.40886368del
NG_028221.1:g.34288del
NM_022098.4:c.645delMANE SELECT
NP_071381.1:p.Ser216fs
NC_000022.10:g.41282372del

Protein change:

S216fs

Links:

dbSNP: rs751910922

NCBI 1000 Genomes Browser:

rs751910922

Molecular consequence:

NM_022098.4:c.645del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Nephronophthisis-like nephropathy 1 (NPHPL1)
Identifiers:: MONDO: MONDO:0013163; MedGen: C3150419; Orphanet: 655; OMIM: 613159

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001478482	Molecular Biology Laboratory, Fundació Puigvert	no assertion criteria provided	Pathogenic (Feb 10, 2021)	unknown	clinical testing
SCV002813909	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 11, 2022)	unknown	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

SCV001478482

Molecular Biology Laboratory, Fundació Puigvert

no assertion criteria provided

Pathogenic
(Feb 10, 2021)

unknown

clinical testing

SCV002813909

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 11, 2022)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
caucasian	unknown	yes	1	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

Details of each submission

From Molecular Biology Laboratory, Fundació Puigvert, SCV001478482.1

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

Description

The XPNPEP3 c.645del p. (Ser216Leufs * 7) variant is a frameshift (LoF ) variant resulting in the creation of a premature protein translation termination codon, so it will theoretically generate a protein of only 221 amino acids instead of the 507 which has the protein Xaa-Pro aminopeptidase 3 (protein encoded by the XPNPEP3 gene). This variant has not been previously described in the scientific literature nor does it appear in The Human Gene Mutation Database. It has only been described in two heterozygous individuals in the gnomAD. Following ACMG classification criteria, it is classified as pathogenic.

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

From Fulgent Genetics, Fulgent Genetics, SCV002813909.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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