NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3]) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Dec 17, 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:: RCV000189556.20

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3])]

NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3])

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.6899ACCAGCTGG[3] (p.2300DQL[3])

HGVS:

NC_000009.12:g.128632263ACCAGCTGG[3]
NG_027748.1:g.84706ACCAGCTGG[3]
NG_034056.1:g.29573AGCTGGTCC[3]
NM_001130438.2:c.6908_6916dup9
NM_001130438.3:c.6899ACCAGCTGG[3]MANE SELECT
NM_001195532.2:c.6824ACCAGCTGG[3]
NM_001363759.2:c.6962ACCAGCTGG[3]
NM_001363765.2:c.6839ACCAGCTGG[3]
NM_001375310.1:c.6986ACCAGCTGG[3]
NM_001375311.2:c.6899ACCAGCTGG[3]
NM_001375312.2:c.6935ACCAGCTGG[3]
NM_001375313.1:c.6881ACCAGCTGG[3]
NM_001375314.2:c.6839ACCAGCTGG[3]
NM_001375318.1:c.6998ACCAGCTGG[3]
NM_003127.4:c.6884ACCAGCTGG[3]
NP_001123910.1:p.2300DQL[3]
NP_001182461.1:p.2275DQL[3]
NP_001350688.1:p.2321DQL[3]
NP_001350694.1:p.2280DQL[3]
NP_001362239.1:p.2329DQL[3]
NP_001362240.1:p.2300DQL[3]
NP_001362241.2:p.2312DQL[3]
NP_001362242.1:p.2294DQL[3]
NP_001362243.1:p.2280DQL[3]
NP_001362247.1:p.2333DQL[3]
NP_003118.2:p.2295DQL[3]
NC_000009.11:g.131394539_131394540insGGACCAGCT
NC_000009.11:g.131394542ACCAGCTGG[3]
NC_000009.12:g.128632260_128632261insGGACCAGCT
NM_001130438.2:c.6908_6916dupACCAGCTGG
NM_001130438.3:c.6908_6916dupMANE SELECT
NM_003127.4:c.6881_6882insGGACCAGCT
p.D2303_L2305dup
p.Leu2305_Gly2306insAspGlnLeu

Links:

OMIM: 182810.0005; dbSNP: rs587784440

NCBI 1000 Genomes Browser:

rs587784440

Molecular consequence:

NM_001130438.3:c.6899ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001195532.2:c.6824ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001363759.2:c.6962ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001363765.2:c.6839ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375310.1:c.6986ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375311.2:c.6899ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375312.2:c.6935ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375313.1:c.6881ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375314.2:c.6839ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375318.1:c.6998ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_003127.4:c.6884ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000243199	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 27, 2022)	germline	clinical testing	Citation Link,
SCV000862913	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Aug 30, 2018)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 29050398, 29337302, 22656320, 25631096 Citation Link,
SCV002023644	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 28, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002818215	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Delineating SPTAN1 associated phenotypes: from isolated epilepsy to encephalopathy with progressive brain atrophy.

Syrbe S, Harms FL, Parrini E, Montomoli M, Mütze U, Helbig KL, Polster T, Albrecht B, Bernbeck U, van Binsbergen E, Biskup S, Burglen L, Denecke J, Heron B, Heyne HO, Hoffmann GF, Hornemann F, Matsushige T, Matsuura R, Kato M, Korenke GC, Kuechler A, et al.

Brain. 2017 Sep 1;140(9):2322-2336. doi: 10.1093/brain/awx195.

PubMed [citation]

PMID:: 29050398
PMCID:: PMC6248409

Critical roles of αII spectrin in brain development and epileptic encephalopathy.

Wang Y, Ji T, Nelson AD, Glanowska K, Murphy GG, Jenkins PM, Parent JM.

J Clin Invest. 2018 Feb 1;128(2):760-773. doi: 10.1172/JCI95743. Epub 2018 Jan 16.

PubMed [citation]

PMID:: 29337302
PMCID:: PMC5785268

See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000243199.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies suggest this variant has a dominant negative effect on neurons, however additional studies are needed to validate the functional effect of this variant (Wang et al., 2018); In-frame duplication of three amino acids in a non-repeat region; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 34440880, 22656320, 29337302, 29050398, 25631096)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000862913.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002023644.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital, SCV002818215.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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