VCV002444508.1 - ClinVar

NM_014706.4(SART3):c.757C>T (p.Arg253Ter)

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.

Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_014706.4(SART3):c.757C>T (p.Arg253Ter)

Variation ID: 2444508 Accession: VCV002444508.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12q23.3 12: 108544451 (GRCh38) [ NCBI UCSC ] 12: 108938227 (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	Jul 1, 2023	Jul 1, 2023	Mar 6, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_014706.4:c.757C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055521.1:p.Arg253Ter	nonsense
NM_001410983.1:c.811C>T	NP_001397912.1:p.Arg271Ter	nonsense
NC_000012.12:g.108544451G>A
NC_000012.11:g.108938227G>A
NG_012155.2:g.21939C>T
LRG_1285:g.21939C>T
LRG_1285t1:c.757C>T	LRG_1285p1:p.Arg253Ter

... more HGVS ... less HGVS

Protein change

R253*, R271*

Other names

Canonical SPDI

NC_000012.12:108544450: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.

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.
SART3		-	-	GRCh38 GRCh37	53	70

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, Neurodevelopmental defects and Developmental delay with 46,XY gonadal dysgenesis	Likely pathogenic (1)	no assertion criteria provided	Mar 6, 2023	RCV003236675.1

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.
Likely pathogenic (Mar 06, 2023)	no assertion criteria provided Method: research	Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY gonadal dysgenesis (Autosomal recessive inheritance) Affected status: yes Allele origin: maternal	Reproductive Development, Murdoch Childrens Research Institute Accession: SCV003842296.1 First in ClinVar: Jul 01, 2023 Last updated: Jul 01, 2023	Publications: PubMed (1) PubMed: 37296101 Comment: This variant was identified in an affected child in trans with a second variant in SART3 c.2299C>T (compound heterozygous). This variant was inherited from a … (more) This variant was identified in an affected child in trans with a second variant in SART3 c.2299C>T (compound heterozygous). This variant was inherited from a heterozgyous unaffected mother. It was identified as part of a larger study that has found biallelic variants in SART3 in nine children from six families with overlapping clinical features. The variant falls in a highly conserved residue within an important HAT protein domain and is predicted to cause a termination in the protein. The variant is extremely rare or absent in population databases. (less) Number of individuals with the variant: 1 Clinical Features: Abnormality of head or neck (present) , Deeply set eye (present) , Abnormality of the nervous system (present) , Severe global developmental delay (present) , … (more) Abnormality of head or neck (present) , Deeply set eye (present) , Abnormality of the nervous system (present) , Severe global developmental delay (present) , Microcephaly (present) , Infantile spasms (present) , Ventriculomegaly (present) , Abnormal cerebral white matter morphology (present) , Hypoplasia of the corpus callosum (present) , Abnormal reproductive system morphology (present) , Abnormality of male external genitalia (present) , Gonadal dysgenesis with female appearance, male (present) , Abnormality of the musculoskeletal system (present) , Hypotonia (present) , Muscle weakness (present) (less)

Comment:

This variant was identified in an affected child in trans with a second variant in SART3 c.2299C>T (compound heterozygous). This variant was inherited from a heterozgyous unaffected mother. It was identified as part of a larger study that has found biallelic variants in SART3 in nine children from six families with overlapping clinical features. The variant falls in a highly conserved residue within an important HAT protein domain and is predicted to cause a termination in the protein. The variant is extremely rare or absent in population databases.

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
Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects.	Ayers KL	Nature communications	2023	PMID: 37296101

Text-mined citations for this variant ...

Record last updated Jul 01, 2023

ClinVar Genomic variation as it relates to human health

NM_014706.4(SART3):c.757C>T (p.Arg253Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...