NM_003179.3(SYP):c.61G>C (p.Val21Leu) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 24, 2023
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:: RCV003236520.1

Allele description [Variation Report for NM_003179.3(SYP):c.61G>C (p.Val21Leu)]

NM_003179.3(SYP):c.61G>C (p.Val21Leu)

Genes:

SYP-AS1:SYP antisense RNA 1 [Gene - HGNC]
SYP:synaptophysin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.23

Genomic location:

Preferred name:

NM_003179.3(SYP):c.61G>C (p.Val21Leu)

HGVS:

NC_000023.11:g.49199009C>G
NG_012532.1:g.6194G>C
NG_012532.2:g.6184G>C
NM_003179.3:c.61G>CMANE SELECT
NP_003170.1:p.Val21Leu
NC_000023.10:g.49055468C>G
NM_003179.2:c.61G>C
NR_046649.1:n.171C>G

Protein change:

V21L

Molecular consequence:

NM_003179.3:c.61G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_046649.1:n.171C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003934865	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (May 24, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003934865

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(May 24, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003934865.1

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

Description

Variant summary: SYP c.61G>C (p.Val21Leu) results in a conservative amino acid change located in the Marvel domain (IPR008253) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 181023 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.61G>C in individuals affected with Intellectual Disability, X-Linked 96 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Jun 24, 2023

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