NM_001379286.1(ZNF423):c.2621C>T (p.Pro874Leu) AND Nephronophthisis 14

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 31, 2019
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:: RCV001229648.9

Allele description [Variation Report for NM_001379286.1(ZNF423):c.2621C>T (p.Pro874Leu)]

NM_001379286.1(ZNF423):c.2621C>T (p.Pro874Leu)

Gene:

ZNF423:zinc finger protein 423 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q12.1

Genomic location:

Preferred name:

NM_001379286.1(ZNF423):c.2621C>T (p.Pro874Leu)

HGVS:

NC_000016.10:g.49636555G>A
NG_032972.2:g.226365C>T
NM_001271620.2:c.2417C>T
NM_001330533.2:c.2246C>T
NM_001379286.1:c.2621C>TMANE SELECT
NM_015069.5:c.2597C>T
NP_001258549.1:p.Pro806Leu
NP_001317462.1:p.Pro749Leu
NP_001366215.1:p.Pro874Leu
NP_055884.2:p.Pro866Leu
NC_000016.9:g.49670466G>A
NM_015069.3:c.2597C>T

Protein change:

P749L

Links:

dbSNP: rs959264947

NCBI 1000 Genomes Browser:

rs959264947

Molecular consequence:

NM_001271620.2:c.2417C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330533.2:c.2246C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379286.1:c.2621C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015069.5:c.2597C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Nephronophthisis 14 (NPHP14)
Identifiers:: MONDO: MONDO:0013916; MedGen: C3539071; Orphanet: 2318; OMIM: 614844

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001402101	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 31, 2019)	germline	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

SCV001402101

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 31, 2019)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001402101.6

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with ZNF423-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with leucine at codon 866 of the ZNF423 protein (p.Pro866Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine.

#	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 16, 2025

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