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NM_020436.5(SALL4):c.2848_2849delinsAA (p.Ser950Lys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 13, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000481093.1

Allele description [Variation Report for NM_020436.5(SALL4):c.2848_2849delinsAA (p.Ser950Lys)]

NM_020436.5(SALL4):c.2848_2849delinsAA (p.Ser950Lys)

Gene:
SALL4:spalt like transcription factor 4 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
20q13.2
Genomic location:
Preferred name:
NM_020436.5(SALL4):c.2848_2849delinsAA (p.Ser950Lys)
HGVS:
  • NC_000020.11:g.51784578_51784579delinsTT
  • NG_008000.1:g.22931_22932delinsAA
  • NM_001318031.2:c.1537_1538delinsAA
  • NM_020436.5:c.2848_2849delinsAAMANE SELECT
  • NP_001304960.1:p.Ser513Lys
  • NP_065169.1:p.Ser950Lys
  • LRG_675t1:c.2848_2849delTCinsAA
  • LRG_675:g.22931_22932delinsAA
  • NC_000020.10:g.50401117_50401118delinsTT
  • NM_020436.3:c.2848_2849delTCinsAA
Protein change:
S513K
Links:
dbSNP: rs1064796498
NCBI 1000 Genomes Browser:
rs1064796498
Molecular consequence:
  • NM_001318031.2:c.1537_1538delinsAA - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020436.5:c.2848_2849delinsAA - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000573279GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Feb 13, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000573279.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.2848_2849delTCinsAA variant in the SALL4 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.2848_2849delTCinsAA variant causes an deletion of two nucleotides and the insertion of two aberrant nucleotides, resulting in the S950L missense change. The S950L variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S950L variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. However, this substitution occurs at a position that is not conserved across species, and in silico analysis predicts this variant likely does not alter the protein structure/function. We interpret c.2848_2849delTCinsAA as a variant of uncertain significance

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022