NM_004187.5(KDM5C):c.2482C>T (p.Arg828Ter) AND Developmental disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 31, 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:: RCV003126757.2

Allele description [Variation Report for NM_004187.5(KDM5C):c.2482C>T (p.Arg828Ter)]

NM_004187.5(KDM5C):c.2482C>T (p.Arg828Ter)

Gene:

KDM5C:lysine demethylase 5C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_004187.5(KDM5C):c.2482C>T (p.Arg828Ter)

HGVS:

NC_000023.11:g.53198524G>A
NG_008085.2:g.31899C>T
NM_001146702.2:c.2281C>T
NM_001282622.3:c.2479C>T
NM_001353978.3:c.2482C>T
NM_001353979.2:c.2479C>T
NM_001353981.2:c.2482C>T
NM_001353982.2:c.2479C>T
NM_001353984.2:c.2482C>T
NM_004187.5:c.2482C>TMANE SELECT
NP_001140174.1:p.Arg761Ter
NP_001269551.1:p.Arg827Ter
NP_001340907.1:p.Arg828Ter
NP_001340908.1:p.Arg827Ter
NP_001340910.1:p.Arg828Ter
NP_001340911.1:p.Arg827Ter
NP_001340913.1:p.Arg828Ter
NP_004178.2:p.Arg828Ter
NC_000023.10:g.53227706G>A
NM_004187.2:c.2482C>T
NM_004187.3:c.2482C>T
NR_148672.2:n.2800C>T
NR_148673.2:n.2797C>T
NR_148674.2:n.2677C>T

Protein change:

R761*

Links:

dbSNP: rs1135401800

NCBI 1000 Genomes Browser:

rs1135401800

Molecular consequence:

NR_148672.2:n.2800C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148673.2:n.2797C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148674.2:n.2677C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001146702.2:c.2281C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282622.3:c.2479C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353978.3:c.2482C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353979.2:c.2479C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353981.2:c.2482C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353982.2:c.2479C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001353984.2:c.2482C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004187.5:c.2482C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Developmental disorder
Identifiers:: MedGen: C0008073

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003803859	Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 31, 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

SCV003803859

Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 31, 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 Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine, SCV003803859.2

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

#	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: Apr 13, 2025

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