VCV002672305.3 - ClinVar

NM_001010942.3(RAP1B):c.451A>G (p.Lys151Glu)

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.

(1)

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001010942.3(RAP1B):c.451A>G (p.Lys151Glu)

Variation ID: 2672305 Accession: VCV002672305.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12q15 12: 68656432 (GRCh38) [ NCBI UCSC ] 12: 69050212 (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 25, 2023	Jun 9, 2024	Mar 6, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001010942.3:c.451A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001010942.1:p.Lys151Glu	missense
NM_001251917.2:c.325A>G	NP_001238846.1:p.Lys109Glu	missense
NM_001251918.2:c.325A>G	NP_001238847.1:p.Lys109Glu	missense
NM_001251921.2:c.394A>G	NP_001238850.1:p.Lys132Glu	missense
NM_001251922.2:c.310A>G	NP_001238851.1:p.Lys104Glu	missense
NM_015646.6:c.451A>G	NP_056461.1:p.Lys151Glu	missense
NC_000012.12:g.68656432A>G
NC_000012.11:g.69050212A>G

... more HGVS ... less HGVS

Protein change

K104E, K109E, K132E

Other names

K151E

Canonical SPDI

NC_000012.12:68656431:A:G

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.

Links

OMIM: 179530.0001 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.
RAP1B		-	-	GRCh38 GRCh37	32	42

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 provided	Uncertain significance (1)	no assertion criteria provided	Mar 6, 2024	RCV003456623.3

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 (Mar 06, 2024)	no assertion criteria provided Method: literature only	VARIANT OF UNKNOWN SIGNIFICANCE Affected status: not provided Allele origin: germline	OMIM Accession: SCV004183562.3 First in ClinVar: Dec 24, 2023 Last updated: Jun 09, 2024	Publications: PubMed (1) PubMed: 26280580 Comment on evidence: This variant is classified as a variant of unknown significance because its contribution to a Kabuki-like syndrome (see 147920) has not been confirmed. In a … (more) This variant is classified as a variant of unknown significance because its contribution to a Kabuki-like syndrome (see 147920) has not been confirmed. In a boy, born of unrelated Turkish parents, with features reminiscent of Kabuki syndrome, Bogershausen et al. (2015) identified a de novo heterozygous c.451A-G transition in the RAP1B gene, resulting in a lys151-to-glu (K151E) substitution at a conserved residue close to the GTP-binding site of RAP1B. The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in the Exome Variant Server or ExAC databases. Expression of the mutation in rap1b-null zebrafish failed to rescue convergent-extension (CE) defects, consistent with a loss of function. There was no evidence for a dominant-negative effect; thus the mutation likely resulted in haploinsufficiency. The patient had growth defects with short stature and microcephaly, developmental delay, seizures, congenital heart defects, and dysmorphic facial features, including long palpebral fissures, arched eyebrows, long eyelashes, dysplastic ears, and strabismus. He also had right tibial shortening and brachyphalangy. The patient had initially been diagnosed clinically with Hadziselimovic syndrome (612946). (less)

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
RAP1-mediated MEK/ERK pathway defects in Kabuki syndrome.	Bögershausen N	The Journal of clinical investigation	2015	PMID: 26280580

Text-mined citations for this variant ...

Record last updated Jun 10, 2024

ClinVar Genomic variation as it relates to human health

NM_001010942.3(RAP1B):c.451A>G (p.Lys151Glu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...