NM_004924.6(ACTN4):c.2620G>A (p.Asp874Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 30, 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:: RCV001913071.4

Allele description [Variation Report for NM_004924.6(ACTN4):c.2620G>A (p.Asp874Asn)]

NM_004924.6(ACTN4):c.2620G>A (p.Asp874Asn)

Gene:

ACTN4:actinin alpha 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.2

Genomic location:

Preferred name:

NM_004924.6(ACTN4):c.2620G>A (p.Asp874Asn)

HGVS:

NC_000019.10:g.38729316G>A
NG_007082.2:g.86630G>A
NM_001322033.2:c.2605G>A
NM_004924.6:c.2620G>AMANE SELECT
NP_001308962.1:p.Asp869Asn
NP_004915.2:p.Asp874Asn
NC_000019.9:g.39219956G>A

Protein change:

D869N

Links:

dbSNP: rs753091185

NCBI 1000 Genomes Browser:

rs753091185

Molecular consequence:

NM_001322033.2:c.2605G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004924.6:c.2620G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Vespula squamosa abdominal-A (abd-A) gene, partial cds
Vespula squamosa abdominal-A (abd-A) gene, partial cds
gi|126508275|gb|EF190787.1|

Nucleotide
cytochrome b, partial (mitochondrion) [Desmodus rotundus]
cytochrome b, partial (mitochondrion) [Desmodus rotundus]
gi|1070715474|gb|AOS60299.1|

Protein
transcription factor C/EBP beta, partial [Homo sapiens]
transcription factor C/EBP beta, partial [Homo sapiens]
gi|595267164|gb|AHM26744.1|

Protein
UNVERIFIED: Phylloscartes difficilis isolate B3992 glyceraldehyde-3-phosphate de...
UNVERIFIED: Phylloscartes difficilis isolate B3992 glyceraldehyde-3-phosphate dehydrogenase (G3PDH) gene, intron 11
gi|1843800547|gb|MT447734.1|

Nucleotide
interferon-induced protein with tetratricopeptide repeats 1, isoform CRA_b [Homo...
interferon-induced protein with tetratricopeptide repeats 1, isoform CRA_b [Homo sapiens]
gi|119570522|gb|EAW50137.1||gnl|WGS |hCP1915952

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002174694	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 30, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30406062, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002174694

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 30, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Genetic Testing for Steroid-Resistant-Nephrotic Syndrome in an Outbred Population.

Varner JD, Chryst-Stangl M, Esezobor CI, Solarin A, Wu G, Lane B, Hall G, Abeyagunawardena A, Matory A, Hunley TE, Lin JJ, Howell D, Gbadegesin R.

Front Pediatr. 2018;6:307. doi: 10.3389/fped.2018.00307.

PubMed [citation]

PMID:: 30406062
PMCID:: PMC6204400

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, SCV002174694.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 1401724). This missense change has been observed in individual(s) with steroid-resistant nephrotic syndrome (PMID: 30406062). This variant is present in population databases (rs753091185, gnomAD 0.008%). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 874 of the ACTN4 protein (p.Asp874Asn).

#	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: Sep 29, 2024

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