NM_000260.4(MYO7A):c.4697C>T (p.Thr1566Met) AND Usher syndrome type 1

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: May 31, 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:: RCV000677317.5

Allele description [Variation Report for NM_000260.4(MYO7A):c.4697C>T (p.Thr1566Met)]

NM_000260.4(MYO7A):c.4697C>T (p.Thr1566Met)

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.4697C>T (p.Thr1566Met)

Other names:

NM_000260.3(MYO7A):c.4697C>T(p.Thr1566Met); NM_001127180.1(MYO7A):c.4583C>T(p.Thr1528Met)

HGVS:

NC_000011.10:g.77199663C>T
NG_009086.2:g.76418C>T
NM_000260.4:c.4697C>TMANE SELECT
NM_001127180.2:c.4583C>T
NM_001369365.1:c.4550C>T
NP_000251.3:p.Thr1566Met
NP_001120652.1:p.Thr1528Met
NP_001356294.1:p.Thr1517Met
LRG_1420t1:c.4697C>T
LRG_1420:g.76418C>T
LRG_1420p1:p.Thr1566Met
NC_000011.9:g.76910708C>T
NG_009086.1:g.76399C>T
NM_000260.3:c.4697C>T
Q13402:p.Thr1566Met
c.4697C>T

Protein change:

T1517M

Links:

UniProtKB: Q13402#VAR_027311; dbSNP: rs41298747

NCBI 1000 Genomes Browser:

rs41298747

Molecular consequence:

NM_000260.4:c.4697C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127180.2:c.4583C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369365.1:c.4550C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Usher syndrome type 1 (USH1)
Synonyms:: Usher syndrome, type I, French variety; Retinitis pigmentosa and congenital deafness
Identifiers:: MONDO: MONDO:0010168; MedGen: C1568247; Orphanet: 231169; Orphanet: 886; OMIM: 276900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000374389	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV000803492	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 31, 2018)	unknown	curation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000374389

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV000803492

SIB Swiss Institute of Bioinformatics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(May 31, 2018)

unknown

curation

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000374389.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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 SIB Swiss Institute of Bioinformatics, SCV000803492.1

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

Description

This variant is interpreted as a Benign, for Usher syndrome 1B, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BP4 => Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

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

Last Updated: Oct 20, 2024

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