NM_015404.4(WHRN):c.1166G>A (p.Gly389Glu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 21, 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:: RCV001236567.6

Allele description [Variation Report for NM_015404.4(WHRN):c.1166G>A (p.Gly389Glu)]

NM_015404.4(WHRN):c.1166G>A (p.Gly389Glu)

Gene:

WHRN:whirlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q32

Genomic location:

Preferred name:

NM_015404.4(WHRN):c.1166G>A (p.Gly389Glu)

HGVS:

NC_000009.12:g.114426211C>T
NG_016700.1:g.84246G>A
NM_001083885.3:c.17G>A
NM_001173425.2:c.1166G>A
NM_015404.4:c.1166G>AMANE SELECT
NP_001077354.2:p.Gly6Glu
NP_001166896.1:p.Gly389Glu
NP_056219.3:p.Gly389Glu
LRG_1094t1:c.1166G>A
LRG_1094:g.84246G>A
LRG_1094p1:p.Gly389Glu
NC_000009.11:g.117188491C>T
NM_015404.3:c.1166G>A

Protein change:

G389E

Links:

dbSNP: rs759109990

NCBI 1000 Genomes Browser:

rs759109990

Molecular consequence:

NM_001083885.3:c.17G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001173425.2:c.1166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015404.4:c.1166G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Plasmodium vivax chromosome 3, whole genome shotgun sequence
Plasmodium vivax chromosome 3, whole genome shotgun sequence
gi|255028013|ref|NC_009908.2||gnl|R S:AAKM|chromo_03

Nucleotide
BIN3-IT1 BIN3 intronic transcript 1 [Homo sapiens]
BIN3-IT1 BIN3 intronic transcript 1 [Homo sapiens]
Gene ID:80094

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001409295	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 21, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001409295

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 21, 2021)

germline

clinical testing

PubMed (3)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001409295.5

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

Description

Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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. ClinVar contains an entry for this variant (Variation ID: 914596). This variant has not been reported in the literature in individuals affected with WHRN-related conditions. This variant is present in population databases (rs759109990, gnomAD 0.0009%). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 389 of the WHRN protein (p.Gly389Glu). This variant also falls at the last nucleotide of exon 4, which is part of the consensus splice site for this exon.

#	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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