VCV000845733.7 - ClinVar

NM_006618.5(KDM5B):c.202C>A (p.Pro68Thr)

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.

(3)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006618.5(KDM5B):c.202C>A (p.Pro68Thr)

Variation ID: 845733 Accession: VCV000845733.7

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1q32.1 1: 202808104 (GRCh38) [ NCBI UCSC ] 1: 202777232 (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	Apr 15, 2020	Oct 8, 2024	Jul 25, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_006618.5:c.202C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_006609.3:p.Pro68Thr	missense
NM_001314042.2:c.202C>A	NP_001300971.1:p.Pro68Thr	missense
NM_001347591.2:c.202C>A	NP_001334520.1:p.Pro68Thr	missense
NM_001399817.1:c.189+13C>A		intron variant
NC_000001.11:g.202808104G>T
NC_000001.10:g.202777232G>T
NG_050659.1:g.6304C>A

... more HGVS ... less HGVS

Protein change

P68T

Other names

Canonical SPDI

NC_000001.11:202808103:G:T

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.

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

Trans-Omics for Precision Medicine (TOPMed) 0.00002

The Genome Aggregation Database (gnomAD) 0.00009

Links

dbSNP: rs369444528 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.
KDM5B		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	309	344
LOC129932249	-	-	-	GRCh38	-	10

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.
Intellectual disability, autosomal recessive 65	Uncertain significance (1)	criteria provided, single submitter	Jul 31, 2021	RCV002479297.1
KDM5B-related disorder	Uncertain significance (1)	no assertion criteria provided	Oct 23, 2023	RCV004553588.2
not provided	Uncertain significance (1)	criteria provided, single submitter	Jul 25, 2022	RCV001048854.4

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.
Uncertain significance (Jul 31, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Intellectual disability, autosomal recessive 65 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002792936.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Uncertain significance (Jul 25, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001212879.2 First in ClinVar: Apr 15, 2020 Last updated: Feb 07, 2023	Comment: This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 68 of the KDM5B protein (p.Pro68Thr). … (more) This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 68 of the KDM5B protein (p.Pro68Thr). This variant is present in population databases (rs369444528, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of KDM5B-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 845733). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. (less)
Uncertain significance (Oct 23, 2023)	no assertion criteria provided Method: clinical testing	KDM5B-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004747166.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: The KDM5B c.202C>A variant is predicted to result in the amino acid substitution p.Pro68Thr. To our knowledge, this variant has not been reported in the … (more) The KDM5B c.202C>A variant is predicted to result in the amino acid substitution p.Pro68Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0052% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-202777232-G-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)

Comment:

This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 68 of the KDM5B protein (p.Pro68Thr). This variant is present in population databases (rs369444528, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of KDM5B-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 845733). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

Comment:

The KDM5B c.202C>A variant is predicted to result in the amino acid substitution p.Pro68Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0052% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-202777232-G-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs369444528 ...

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 Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_006618.5(KDM5B):c.202C>A (p.Pro68Thr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs369444528 ...