NM_001353921.2(ARHGEF9):c.419G>A (p.Cys140Tyr) AND Developmental and epileptic encephalopathy, 8

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 8, 2022
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:: RCV002286493.1

Allele description [Variation Report for NM_001353921.2(ARHGEF9):c.419G>A (p.Cys140Tyr)]

NM_001353921.2(ARHGEF9):c.419G>A (p.Cys140Tyr)

Gene:

ARHGEF9:Cdc42 guanine nucleotide exchange factor 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq11.1

Genomic location:

Preferred name:

NM_001353921.2(ARHGEF9):c.419G>A (p.Cys140Tyr)

HGVS:

NC_000023.11:g.63697288C>T
NG_016975.1:g.93259G>A
NM_001173479.2:c.239G>A
NM_001173480.2:c.92G>A
NM_001330495.2:c.335G>A
NM_001353921.2:c.419G>AMANE SELECT
NM_001353922.2:c.419G>A
NM_001353923.1:c.437G>A
NM_001353924.2:c.218G>A
NM_001353926.2:c.218G>A
NM_001353927.2:c.335G>A
NM_001353928.2:c.398G>A
NM_001369030.1:c.398G>A
NM_001369031.1:c.398G>A
NM_001369032.1:c.398G>A
NM_001369033.1:c.335G>A
NM_001369034.1:c.335G>A
NM_001369035.1:c.335G>A
NM_001369036.1:c.335G>A
NM_001369037.1:c.335G>A
NM_001369038.1:c.335G>A
NM_001369039.1:c.218G>A
NM_001369040.1:c.218G>A
NM_001369041.1:c.335G>A
NM_001369042.1:c.92G>A
NM_001369043.1:c.335G>A
NM_001369044.1:c.335G>A
NM_001369045.1:c.-17G>A
NM_015185.3:c.398G>A
NP_001166950.1:p.Cys80Tyr
NP_001166951.1:p.Cys31Tyr
NP_001317424.1:p.Cys112Tyr
NP_001340850.1:p.Cys140Tyr
NP_001340851.1:p.Cys140Tyr
NP_001340852.1:p.Cys146Tyr
NP_001340853.1:p.Cys73Tyr
NP_001340855.1:p.Cys73Tyr
NP_001340856.1:p.Cys112Tyr
NP_001340857.1:p.Cys133Tyr
NP_001355959.1:p.Cys133Tyr
NP_001355960.1:p.Cys133Tyr
NP_001355961.1:p.Cys133Tyr
NP_001355962.1:p.Cys112Tyr
NP_001355963.1:p.Cys112Tyr
NP_001355964.1:p.Cys112Tyr
NP_001355965.1:p.Cys112Tyr
NP_001355966.1:p.Cys112Tyr
NP_001355967.1:p.Cys112Tyr
NP_001355968.1:p.Cys73Tyr
NP_001355969.1:p.Cys73Tyr
NP_001355970.1:p.Cys112Tyr
NP_001355971.1:p.Cys31Tyr
NP_001355972.1:p.Cys112Tyr
NP_001355973.1:p.Cys112Tyr
NP_056000.1:p.Cys133Tyr
NC_000023.10:g.62917168C>T

Protein change:

C112Y

Molecular consequence:

NM_001369045.1:c.-17G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001173479.2:c.239G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001173480.2:c.92G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330495.2:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353921.2:c.419G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353922.2:c.419G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353923.1:c.437G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353924.2:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353926.2:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353927.2:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353928.2:c.398G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369030.1:c.398G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369031.1:c.398G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369032.1:c.398G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369033.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369034.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369035.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369036.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369037.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369038.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369039.1:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369040.1:c.218G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369041.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369042.1:c.92G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369043.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369044.1:c.335G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015185.3:c.398G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 8 (DEE8)
Synonyms:: HYPEREKPLEXIA AND EPILEPSY; Early infantile epileptic encephalopathy 8
Identifiers:: MONDO: MONDO:0010375; MedGen: C1845102; Orphanet: 163985; Orphanet: 2076; OMIM: 300607

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002576460	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 8, 2022)	de novo	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

SCV002576460

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 8, 2022)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

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 Institute of Human Genetics, University of Leipzig Medical Center, SCV002576460.1

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

Description

This variant was identified as hemizygous._x000D_ Criteria applied: PS2_MOD, PM1, PM2_SUP, PP3

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

Last Updated: Aug 5, 2023

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