NM_153676.4(USH1C):c.2611G>A (p.Ala871Thr) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Sep 19, 2016
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:: RCV000041285.17

Allele description [Variation Report for NM_153676.4(USH1C):c.2611G>A (p.Ala871Thr)]

NM_153676.4(USH1C):c.2611G>A (p.Ala871Thr)

Gene:

USH1C:USH1 protein network component harmonin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.1

Genomic location:

Preferred name:

NM_153676.4(USH1C):c.2611G>A (p.Ala871Thr)

Other names:

p.A871T:GCT>ACT

HGVS:

NC_000011.10:g.17495613C>T
NG_011883.2:g.53804G>A
NM_001297764.2:c.1589+1145G>A
NM_005709.4:c.1646+1145G>A
NM_153676.4:c.2611G>AMANE SELECT
NP_710142.1:p.Ala871Thr
NC_000011.9:g.17517160C>T
NG_011883.1:g.53804G>A
NM_005709.3:c.1646+1145G>A
NM_153676.2:c.2611G>A
NM_153676.3:c.2611G>A
c.2611G>A

Protein change:

A871T

Links:

dbSNP: rs56165709

NCBI 1000 Genomes Browser:

rs56165709

Molecular consequence:

NM_001297764.2:c.1589+1145G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_005709.4:c.1646+1145G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_153676.4:c.2611G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000064976	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (May 15, 2012)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11139240, 24033266
SCV000169729	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 13, 2013)	germline	clinical testing	Citation Link,
SCV000345732	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Sep 19, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000064976

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(May 15, 2012)

germline

clinical testing

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

SCV000169729

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(May 13, 2013)

germline

clinical testing

Citation Link,

SCV000345732

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Sep 19, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	14	14	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of three novel mutations in the USH1C gene and detection of thirty-one polymorphisms used for haplotype analysis.

Zwaenepoel I, Verpy E, Blanchard S, Meins M, Apfelstedt-Sylla E, Gal A, Petit C.

Hum Mutat. 2001;17(1):34-41.

PubMed [citation]

PMID:: 11139240

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000064976.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	14	not provided	not provided	clinical testing	PubMed (2)

Description

Ala871Thr in Exon 26 of USH1C: This variant is not expected to have clinical sig nificance because it has been identified in 0.5% (35/7020) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs56165709). In addition, this variant has be en reported in one individual with Usher type 1 who carried two other truncating USH1C variants assumed to explain disease, one in cis with Ala871Thr (Zwaenepoe le 2001).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		14	not provided	14	not provided

From GeneDx, SCV000169729.10

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000345732.4

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

#	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		1	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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