NM_014140.4(SMARCAL1):c.1975C>T (p.Arg659Cys) AND Atypical hemolytic uremic syndrome

Clinical significance:Uncertain significance (Last evaluated: Oct 24, 2018)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_014140.4(SMARCAL1):c.1975C>T (p.Arg659Cys)]

NM_014140.4(SMARCAL1):c.1975C>T (p.Arg659Cys)

SMARCAL1:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_014140.4(SMARCAL1):c.1975C>T (p.Arg659Cys)
  • NC_000002.12:g.216450969C>T
  • NG_009771.1:g.43556C>T
  • NM_001127207.2:c.1975C>T
  • NM_014140.4:c.1975C>TMANE SELECT
  • NP_001120679.1:p.Arg659Cys
  • NP_054859.2:p.Arg659Cys
  • LRG_108:g.43556C>T
  • NC_000002.11:g.217315692C>T
  • NM_001127207.1:c.1975C>T
Protein change:
Molecular consequence:
  • NM_001127207.2:c.1975C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014140.4:c.1975C>T - missense variant - [Sequence Ontology: SO:0001583]


Atypical hemolytic uremic syndrome (AHUS)
MONDO: MONDO:0016244; MedGen: C2931788; OMIM: PS235400

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001449448Sydney Genome Diagnostics,Children's Hospital Westmeadno assertion criteria providedUncertain significance
(Oct 24, 2018)
unknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Sydney Genome Diagnostics,Children's Hospital Westmead, SCV001449448.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided


This patient is heterozygous for a variant of unknown clinical significance (VOUS), c.1975C>T p.(Arg659Cys), in exon 12 of the SMARCAL1 gene. To our knowledge, this variant has not been previously reported in the literature to be disease causing. This variant (dbSNP: rs148893764) has been reported in the ExAC database with a very low allele frequency (1 out of 121206 alleles). In silico analysis (Alamut Visual v2.6) using PolyPhen2, SIFT, Align GVGD and Mutation Taster all suggest that this variant to be likely pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2021

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