NM_153700.2(STRC):c.4675C>T (p.Gln1559Ter) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Sep 12, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000756727.11

Allele description [Variation Report for NM_153700.2(STRC):c.4675C>T (p.Gln1559Ter)]

NM_153700.2(STRC):c.4675C>T (p.Gln1559Ter)

Gene:

STRC:stereocilin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.3

Genomic location:

Preferred name:

NM_153700.2(STRC):c.4675C>T (p.Gln1559Ter)

HGVS:

NC_000015.10:g.43601422G>A
NG_011636.1:g.22379C>T
NM_153700.2:c.4675C>TMANE SELECT
NP_714544.1:p.Gln1559Ter
NC_000015.9:g.43893620G>A
p.Gln1559*

Protein change:

Q1559*

Links:

dbSNP: rs147717802

NCBI 1000 Genomes Browser:

rs147717802

Molecular consequence:

NM_153700.2:c.4675C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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JP 2021052748-A/67: LETTUCE PLANTS HAVING RESISTANCE TO NASONOVIA RIBISNIGRI BIO...
JP 2021052748-A/67: LETTUCE PLANTS HAVING RESISTANCE TO NASONOVIA RIBISNIGRI BIOTYPE NR:1
gi|2751663642|dbj|PA659884.1||pat|J 1052748|67

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000884619	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely pathogenic (Jul 11, 2017)	germline	clinical testing	Citation Link,
SCV001145829	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Sep 12, 2018)	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

SCV000884619

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely pathogenic
(Jul 11, 2017)

germline

clinical testing

Citation Link,

SCV001145829

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely pathogenic
(Sep 12, 2018)

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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884619.1

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

Description

The c.4675C>T variant (rs147717802) has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. The c.4675C>T variant creates a termination codon in the STRC protein at codon 1559 in exon 24 out of 29 which is predicted to result in a truncated or absent protein product. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.001 percent (identified on 3 out of 277,104 chromosomes). Based on these observations, the c.4675C>T has been classified as likely pathogenic.

#	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

From Athena Diagnostics, SCV001145829.1

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

Description

The variant creates a premature nonsense codon, and is therefore predicted to significantly disrupt the protein structure. The best available variant frequency is uninformative because it is below the disease allele frequency.

#	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 7, 2024

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