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NM_001130438.3(SPTAN1):c.3051G>A (p.Pro1017=) AND Developmental and epileptic encephalopathy, 5

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Aug 18, 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:
RCV001808365.11

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.3051G>A (p.Pro1017=)]

NM_001130438.3(SPTAN1):c.3051G>A (p.Pro1017=)

Gene:
SPTAN1:spectrin alpha, non-erythrocytic 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.11
Genomic location:
Preferred name:
NM_001130438.3(SPTAN1):c.3051G>A (p.Pro1017=)
Other names:
p.P1017P:CCG>CCA
HGVS:
  • NC_000009.12:g.128591521G>A
  • NG_027748.1:g.43964G>A
  • NM_001130438.3:c.3051G>AMANE SELECT
  • NM_001195532.2:c.3051G>A
  • NM_001363759.2:c.3051G>A
  • NM_001363765.2:c.3051G>A
  • NM_003127.4:c.3051G>A
  • NP_001123910.1:p.Pro1017=
  • NP_001182461.1:p.Pro1017=
  • NP_001350688.1:p.Pro1017=
  • NP_001350694.1:p.Pro1017=
  • NP_003118.2:p.Pro1017=
  • NC_000009.11:g.131353800G>A
  • NM_001130438.2:c.3051G>A
Links:
dbSNP: rs140279996
NCBI 1000 Genomes Browser:
rs140279996
Molecular consequence:
  • NM_001130438.3:c.3051G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001195532.2:c.3051G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363759.2:c.3051G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363765.2:c.3051G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_003127.4:c.3051G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Developmental and epileptic encephalopathy, 5 (DEE5)
Synonyms:
Early infantile epileptic encephalopathy 5
Identifiers:
MONDO: MONDO:0013277; MedGen: C3150731; Orphanet: 3451; OMIM: 613477

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002056652Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jul 15, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003920507Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Aug 18, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genome-Nilou Lab, SCV002056652.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920507.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.4% (190/41396) (https://gnomad.broadinstitute.org/variant/9-128591521-G-A?dataset=gnomad_r3). This variant is present in ClinVar, with several labs classifying this variant as Benign (Variation ID:139282). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign.

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

Last Updated: Jul 7, 2024