VCV003358932.1 - ClinVar

NM_001042750.2(STAG2):c.1788_1789insGG (p.Leu597fs)

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_001042750.2(STAG2):c.1788_1789insGG (p.Leu597fs)

Variation ID: 3358932 Accession: VCV003358932.1

Type and length

Insertion, -

Location

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	Oct 13, 2024	Oct 13, 2024	Oct 8, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001042750.2:c.1788_1789insGG MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001036215.1:p.Leu597fs	frameshift
NM_001042749.2:c.1788_1789insGG	NP_001036214.1:p.Leu597fs	frameshift
NM_001042751.2:c.1788_1789insGG	NP_001036216.1:p.Leu597fs	frameshift
NM_001282418.2:c.1788_1789insGG	NP_001269347.1:p.Leu597fs	frameshift
NM_001375366.1:c.1788_1789insGG	NP_001362295.1:p.Leu597fs	frameshift
NM_001375367.1:c.1788_1789insGG	NP_001362296.1:p.Leu597fs	frameshift
NM_001375368.1:c.1788_1789insGG	NP_001362297.1:p.Leu597fs	frameshift
NM_001375369.1:c.1788_1789insGG	NP_001362298.1:p.Leu597fs	frameshift
NM_001375370.1:c.1788_1789insGG	NP_001362299.1:p.Leu597fs	frameshift
NM_001375371.1:c.1788_1789insGG	NP_001362300.1:p.Leu597fs	frameshift
NM_001375372.1:c.1788_1789insGG	NP_001362301.1:p.Leu597fs	frameshift
NM_001375373.1:c.1788_1789insGG	NP_001362302.1:p.Leu597fs	frameshift
NM_001375374.1:c.1788_1789insGG	NP_001362303.1:p.Leu597fs	frameshift
NM_001375375.1:c.1788_1789insGG	NP_001362304.1:p.Leu597fs	frameshift
NM_001375376.1:c.1788_1789insGG	NP_001362305.1:p.Leu597fs	frameshift
NM_001375377.1:c.1788_1789insGG	NP_001362306.1:p.Leu597fs	frameshift
NM_006603.5:c.1788_1789insGG	NP_006594.3:p.Leu597fs	frameshift
NC_000023.11:g.124063172_124063173insGG
NC_000023.10:g.123197022_123197023insGG
NG_033796.2:g.107613_107614insGG
LRG_782:g.107613_107614insGG
LRG_782t1:c.1788_1789insGG	LRG_782p1:p.Leu597fs
LRG_782t2:c.1788_1789insGG	LRG_782p2:p.Leu597Glyfs
LRG_782t3:c.1788_1789insGG	LRG_782p3:p.Leu597Glyfs

... more HGVS ... less HGVS

Protein change

L597fs

Other names

Canonical SPDI

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

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.
STAG2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	586	775

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.
Mullegama-Klein-Martinez syndrome	Pathogenic (1)	criteria provided, single submitter	Oct 8, 2024	RCV004759470.1

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 (Oct 08, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Mullegama-Klein-Martinez syndrome Affected status: yes Allele origin: de novo	Department of Human Genetics, Hannover Medical School Accession: SCV005367999.1 First in ClinVar: Oct 13, 2024 Last updated: Oct 13, 2024	Comment: ACMG: PVS1, PS2_Supporting, PM2_Supporting Clinical Features: Microcephaly (present) , Retrognathia (present) , Low anterior hairline (present) , Strabismus (present) , Sacral dimple (present) , Cutis marmorata (present) , Global developmental delay … (more) Microcephaly (present) , Retrognathia (present) , Low anterior hairline (present) , Strabismus (present) , Sacral dimple (present) , Cutis marmorata (present) , Global developmental delay (present) , Congenital laryngomalacia (present) , Depressed nasal bridge (present) , Low hanging columella (present) , Gemination (present) , Prominent eyelashes (present) , Abnormal myelination (present) , Long fingers (present) (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

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 this variant ...

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_001042750.2(STAG2):c.1788_1789insGG (p.Leu597fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...