VCV002126450.2 - ClinVar

NM_001242.5(CD27):c.256del (p.His86fs)

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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001242.5(CD27):c.256del (p.His86fs)

Variation ID: 2126450 Accession: VCV002126450.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 12p13.31 12: 6445543 (GRCh38) [ NCBI UCSC ] 12: 6554709 (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	Feb 8, 2023	Feb 20, 2024	Apr 15, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001242.5:c.256del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001233.2:p.His86fs	frameshift
NM_001413263.1:c.256delC	NP_001400192.1:p.His86Thrfs	frameshift
NM_001413265.1:c.256delC	NP_001400194.1:p.His86Thrfs	frameshift
NM_001413266.1:c.-195delC
NM_001413267.1:c.-283delC
NM_001413268.1:c.-195delC
NR_182125.1:n.397delC
NR_182126.1:n.397delC
NR_182127.1:n.291delC
NR_182128.1:n.397delC
NC_000012.12:g.6445543del
NC_000012.11:g.6554709del
NG_031995.1:g.5659del
NG_125026.1:g.553del
LRG_357:g.5659del
LRG_357t1:c.256del	LRG_357p1:p.His86Thrfs

... more HGVS ... less HGVS

Protein change

H86fs

Other names

Canonical SPDI

NC_000012.12:6445542:C:

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

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.
CD27		-	-	GRCh38 GRCh37	4	257
CD27-AS1	-	-	-	GRCh38	-	215

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.
Lymphoproliferative syndrome 2	Pathogenic (1)	criteria provided, single submitter	Apr 15, 2022	RCV003051666.3

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.
Pathogenic (Apr 15, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Lymphoproliferative syndrome 2 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003343445.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Publications: PubMed (1) PubMed: 25843314 Comment: This sequence change creates a premature translational stop signal (p.His86Thrfs43) in the CD27 gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.His86Thrfs43) in the CD27 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CD27 are known to be pathogenic (PMID: 25843314). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CD27-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change creates a premature translational stop signal (p.His86Thrfs*43) in the CD27 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CD27 are known to be pathogenic (PMID: 25843314). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CD27-related conditions. For these reasons, this variant has been classified as Pathogenic.

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
Novel mutations in TNFRSF7/CD27: Clinical, immunologic, and genetic characterization of human CD27 deficiency.	Alkhairy OK	The Journal of allergy and clinical immunology	2015	PMID: 25843314

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001242.5(CD27):c.256del (p.His86fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...