NM_000260.4(MYO7A):c.6062A>G (p.Lys2021Arg) AND Rare genetic deafness

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 5, 2015
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:: RCV000223094.11

Allele description [Variation Report for NM_000260.4(MYO7A):c.6062A>G (p.Lys2021Arg)]

NM_000260.4(MYO7A):c.6062A>G (p.Lys2021Arg)

Gene:

MYO7A:myosin VIIA [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.5

Genomic location:

Preferred name:

NM_000260.4(MYO7A):c.6062A>G (p.Lys2021Arg)

HGVS:

NC_000011.10:g.77211162A>G
NG_009086.2:g.87917A>G
NM_000260.4:c.6062A>GMANE SELECT
NM_001127180.2:c.5948A>G
NM_001369365.1:c.5915A>G
NP_000251.3:p.Lys2021Arg
NP_001120652.1:p.Lys1983Arg
NP_001356294.1:p.Lys1972Arg
LRG_1420t1:c.6062A>G
LRG_1420:g.87917A>G
LRG_1420p1:p.Lys2021Arg
NC_000011.9:g.76922207A>G
NG_009086.1:g.87898A>G
NM_000260.3:c.6062A>G
NM_000260.4(MYO7A):c.6062A>GMANE SELECT

Protein change:

K1972R

Links:

dbSNP: rs876657655

NCBI 1000 Genomes Browser:

rs876657655

Molecular consequence:

NM_000260.4:c.6062A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127180.2:c.5948A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369365.1:c.5915A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Rare genetic deafness
Identifiers:: MedGen: C5680250; Orphanet: 96210

Recent activity

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NP_040335 (0)
dbVar
Tssr69988 AND (alive[prop]) (0)
Gene
Dopamine receptor D3 [Homo sapiens]
Dopamine receptor D3 [Homo sapiens]
gi|118764187|gb|AAI28124.1|

Protein
RC0-HT0022-010799-001-D07 HT0022 Homo sapiens cDNA, mRNA sequence
RC0-HT0022-010799-001-D07 HT0022 Homo sapiens cDNA, mRNA sequence
gi|5435670|gnl|dbEST|2904211|gb|AI8 .1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000271250	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely pathogenic (Nov 5, 2015)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21436283, 24033266

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000271250

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely pathogenic
(Nov 5, 2015)

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	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Four-year follow-up of diagnostic service in USH1 patients.

Roux AF, Faugère V, Vaché C, Baux D, Besnard T, Léonard S, Blanchet C, Hamel C, Mondain M, Gilbert-Dussardier B, Edery P, Lacombe D, Bonneau D, Holder-Espinasse M, Ambrosetti U, Journel H, David A, Lina-Granade G, Malcolm S, Claustres M.

Invest Ophthalmol Vis Sci. 2011 Jun 8;52(7):4063-71. doi: 10.1167/iovs.10-6869.

PubMed [citation]

PMID:: 21436283

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, SCV000271250.2

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

Description

The p.Lys2021Arg variant in MYO7A has been reported in one individual with type I Usher syndrome who was compound heterozygous for a second likely pathogenic va riant in MYO7A (Roux 2011). This variant was absent from large population studie s. Computational prediction tools and conservation analyses suggest that the p.L ys2021Arg variant may impact the protein. In summary, although additional studie s are required to fully establish its clinical significance, this variant is lik ely pathogenic based on the previous report in an individual with Usher syndrome .

#	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		1	not provided	1	not provided

Last Updated: Sep 16, 2024

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