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NM_001130438.3(SPTAN1):c.6917GCATGC[3] (p.Arg2308_Met2309dup) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Dec 1, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000189545.13

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.6917GCATGC[3] (p.Arg2308_Met2309dup)]

NM_001130438.3(SPTAN1):c.6917GCATGC[3] (p.Arg2308_Met2309dup)

Gene:
SPTAN1:spectrin alpha, non-erythrocytic 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
9q34.11
Genomic location:
Preferred name:
NM_001130438.3(SPTAN1):c.6917GCATGC[3] (p.Arg2308_Met2309dup)
HGVS:
  • NC_000009.12:g.128632281GCATGC[3]
  • NG_027748.1:g.84724GCATGC[3]
  • NG_034056.1:g.29559GCATGC[3]
  • NM_001130438.3:c.6917GCATGC[3]MANE SELECT
  • NM_001195532.2:c.6842GCATGC[3]
  • NM_001363759.2:c.6980GCATGC[3]
  • NM_001363765.2:c.6857GCATGC[3]
  • NM_001375310.1:c.7004GCATGC[3]
  • NM_001375311.2:c.6917GCATGC[3]
  • NM_001375312.2:c.6953GCATGC[3]
  • NM_001375313.1:c.6899GCATGC[3]
  • NM_001375314.2:c.6857GCATGC[3]
  • NM_001375318.1:c.7016GCATGC[3]
  • NM_003127.4:c.6902GCATGC[3]
  • NP_001123910.1:p.Arg2308_Met2309dup
  • NP_001182461.1:p.Arg2283_Met2284dup
  • NP_001350688.1:p.Arg2329_Met2330dup
  • NP_001350694.1:p.Arg2288_Met2289dup
  • NP_001362239.1:p.Arg2337_Met2338dup
  • NP_001362240.1:p.Arg2308_Met2309dup
  • NP_001362241.2:p.Arg2320_Met2321dup
  • NP_001362242.1:p.Arg2302_Met2303dup
  • NP_001362243.1:p.Arg2288_Met2289dup
  • NP_001362247.1:p.Arg2341_Met2342dup
  • NP_003118.2:p.Arg2303_Met2304dup
  • NC_000009.11:g.131394560GCATGC[3]
  • NM_001130438.2:c.6923_6928dupGCATGC
  • NM_001130438.3:c.6923_6928dupMANE SELECT
  • p.R2308_M2309dup
Links:
OMIM: 182810.0002; dbSNP: rs796053335
NCBI 1000 Genomes Browser:
rs796053335
Molecular consequence:
  • NM_001130438.3:c.6917GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001195532.2:c.6842GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001363759.2:c.6980GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001363765.2:c.6857GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001375310.1:c.7004GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001375311.2:c.6917GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001375312.2:c.6953GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001375313.1:c.6899GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001375314.2:c.6857GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001375318.1:c.7016GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_003127.4:c.6902GCATGC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000243188GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Aug 27, 2013)
germlineclinical testing

Citation Link,

SCV002821970CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Dec 1, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000243188.3

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

Description

c.6923_6928dupGCATGC: p.Arg2308_Met2309dup (R2308_M2309dup) in exon 53 of the SPTAN1 gene (NM_001130438.1). The normal sequence with the bases that are duplicated in braces is: CATG{CGCATG}. The c.6923_6928dupGCATGC mutation in the SPTAN1 gene has been previously reported as a de novo mutation in an individual with early-onset West syndrome and cerebellar hypomyelination (Saitsu et al., 2010). It results in an in-frame duplication of two highly conserved amino acids in the last spectrin repeat of the protein, and functional studies indicate the c.6923_6928dupGCATGC mutation leads to the aggregation of alpha/beta spectrin heterodimers (Saitsu et al., 2010). Therefore, c.6923_6928dupGCATGC is interpreted as pathogenic. The variant is found in INFANT-EPI panel(s).

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

From CeGaT Center for Human Genetics Tuebingen, SCV002821970.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

SPTAN1: PS2, PM2, PM4, PS4:Moderate, PP4

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 15, 2024