NM_015404.4(WHRN):c.2548G>A (p.Gly850Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2021
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:: RCV001337308.7

Allele description [Variation Report for NM_015404.4(WHRN):c.2548G>A (p.Gly850Ser)]

NM_015404.4(WHRN):c.2548G>A (p.Gly850Ser)

Gene:

WHRN:whirlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q32

Genomic location:

Preferred name:

NM_015404.4(WHRN):c.2548G>A (p.Gly850Ser)

HGVS:

NC_000009.12:g.114402930C>T
NG_016700.1:g.107527G>A
NM_001083885.3:c.1399G>A
NM_001173425.2:c.2545G>A
NM_001346890.1:c.1495G>A
NM_015404.4:c.2548G>AMANE SELECT
NP_001077354.2:p.Gly467Ser
NP_001166896.1:p.Gly849Ser
NP_001333819.1:p.Gly499Ser
NP_056219.3:p.Gly850Ser
LRG_1094t1:c.2548G>A
LRG_1094:g.107527G>A
LRG_1094p1:p.Gly850Ser
NC_000009.11:g.117165210C>T

Protein change:

G467S

Links:

dbSNP: rs766123228

NCBI 1000 Genomes Browser:

rs766123228

Molecular consequence:

NM_001083885.3:c.1399G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001173425.2:c.2545G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346890.1:c.1495G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015404.4:c.2548G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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zinc finger protein 544 isoform 12 [Homo sapiens]
zinc finger protein 544 isoform 12 [Homo sapiens]
gi|1913184548|ref|NP_001374339.1|

Protein
zinc finger protein 544 isoform 14 [Homo sapiens]
zinc finger protein 544 isoform 14 [Homo sapiens]
gi|1913184314|ref|NP_001374345.1|

Protein
Homo sapiens zinc finger protein 544 (ZNF544), transcript variant 29, mRNA
Homo sapiens zinc finger protein 544 (ZNF544), transcript variant 29, mRNA
gi|1913184335|ref|NM_001387398.1|

Nucleotide
zinc finger protein 544 isoform 27 [Homo sapiens]
zinc finger protein 544 isoform 27 [Homo sapiens]
gi|2307937330|ref|NP_001399103.1|

Protein
zinc finger protein 544 isoform 11 [Homo sapiens]
zinc finger protein 544 isoform 11 [Homo sapiens]
gi|1913184457|ref|NP_001374337.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001530904	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2021)	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

SCV001530904

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2021)

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, SCV001530904.4

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

Description

This sequence change replaces glycine with serine at codon 850 of the WHRN protein (p.Gly850Ser). The glycine residue is highly conserved and there is a small physicochemical difference between glycine and serine. This variant is present in population databases (rs766123228, ExAC 0.01%). This variant has not been reported in the literature in individuals affected with WHRN-related conditions. 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

#	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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