NM_004252.5(NHERF1):c.325_326delinsTT (p.Glu109Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 16, 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:: RCV003732850.2

Allele description [Variation Report for NM_004252.5(NHERF1):c.325_326delinsTT (p.Glu109Leu)]

NM_004252.5(NHERF1):c.325_326delinsTT (p.Glu109Leu)

Genes:

NHERF1:NHERF family PDZ scaffold protein 1 [Gene - OMIM - HGNC]
SLC9A3R1-AS1:SLC9A3R1 antisense RNA 1 [Gene - HGNC]

Variant type:

Indel

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_004252.5(NHERF1):c.325_326delinsTT (p.Glu109Leu)

HGVS:

NC_000017.11:g.74749171_74749172delinsTT
NG_013022.1:g.5548_5549delinsTT
NG_137513.1:g.206_207delinsTT
NM_004252.5:c.325_326delinsTTMANE SELECT
NP_004243.1:p.Glu109Leu
NC_000017.10:g.72745310_72745311delinsTT
NR_187307.1:n.696_697delinsAA

Protein change:

E109L

Molecular consequence:

NM_004252.5:c.325_326delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NR_187307.1:n.696_697delinsAA - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004520465	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 16, 2023)	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

SCV004520465

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 16, 2023)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004520465.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals affected with SLC9A3R1-related conditions. This variant is present in population databases (no rsID available, gnomAD 5%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces glutamic acid, which is acidic and polar, with leucine, which is neutral and non-polar, at codon 109 of the SLC9A3R1 protein (p.Glu109Leu).

#	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: Sep 29, 2024

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