VCV000281538.19 - ClinVar

NM_004187.5(KDM5C):c.108C>T (p.Pro36=)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(6)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_004187.5(KDM5C):c.108C>T (p.Pro36=)

Variation ID: 281538 Accession: VCV000281538.19

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xp11.22 X: 53224782 (GRCh38) [ NCBI UCSC ] X: 53253964 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 6, 2016	Oct 8, 2024	Aug 11, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NM_004187.5:c.108C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_004178.2:p.Pro36=	synonymous
NM_001146702.2:c.108C>T	NP_001140174.1:p.Pro36=	synonymous
NM_001282622.3:c.108C>T	NP_001269551.1:p.Pro36=	synonymous
NM_001353978.3:c.108C>T	NP_001340907.1:p.Pro36=	synonymous
NM_001353979.2:c.108C>T	NP_001340908.1:p.Pro36=	synonymous
NM_001353981.2:c.108C>T	NP_001340910.1:p.Pro36=	synonymous
NM_001353982.2:c.108C>T	NP_001340911.1:p.Pro36=	synonymous
NM_001353984.2:c.108C>T	NP_001340913.1:p.Pro36=	synonymous
NR_148672.2:n.426C>T		non-coding transcript variant
NR_148673.2:n.426C>T		non-coding transcript variant
NR_148674.2:n.426C>T		non-coding transcript variant
NC_000023.11:g.53224782G>A
NC_000023.10:g.53253964G>A
NG_008085.2:g.5641C>T
NG_021296.2:g.101569C>T
LRG_1194:g.101569C>T

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000023.11:53224781:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00079 (A)

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD), exomes 0.00020

Exome Aggregation Consortium (ExAC) 0.00031

1000 Genomes Project 30x 0.00062

Trans-Omics for Precision Medicine (TOPMed) 0.00065

The Genome Aggregation Database (gnomAD) 0.00077

1000 Genomes Project 0.00079

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00095

Links

ClinGen: CA10419752 dbSNP: rs139309563 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
KDM5C		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	748	916
LOC130068308	-	-	-	GRCh38	-	84

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign/Likely benign (2)	criteria provided, multiple submitters, no conflicts	Nov 18, 2016	RCV000333922.10
not provided	Benign (1)	criteria provided, single submitter	Aug 11, 2021	RCV000863772.7
Inborn genetic diseases	Likely benign (1)	criteria provided, single submitter	Apr 14, 2019	RCV002446513.2
Spastic paraplegia	Benign (1)	criteria provided, single submitter	May 29, 2018	RCV001513377.6
KDM5C-related disorder	Likely benign (1)	no assertion criteria provided	Aug 13, 2019	RCV003909911.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Jun 29, 2015)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000332368.4 First in ClinVar: Dec 06, 2016 Last updated: May 03, 2018	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KDM5C Number of individuals with the variant: 1 Sex: mixed
Likely benign (Nov 18, 2016)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not specified Affected status: no Allele origin: germline	Genetic Services Laboratory, University of Chicago Accession: SCV000595324.1 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (May 29, 2018)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Spastic paraplegia Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001720987.2 First in ClinVar: Jun 15, 2021 Last updated: Apr 09, 2023
Benign (Aug 11, 2021)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001985664.2 First in ClinVar: Nov 06, 2021 Last updated: Mar 04, 2023
Likely benign (Apr 14, 2019)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002732050.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more) This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
Likely benign (Aug 13, 2019)	no assertion criteria provided Method: clinical testing	KDM5C-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004725888.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Comment:

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=KDM5C	-	-	-	-

Text-mined citations for rs139309563 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 13, 2024

ClinVar Genomic variation as it relates to human health

NM_004187.5(KDM5C):c.108C>T (p.Pro36=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs139309563 ...