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NM_000401.3(EXT2):c.110C>T (p.Ser37Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Likely pathogenic(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 20, 2020)
Last evaluated:
Jul 7, 2018
Accession:
VCV000304572.4
Variation ID:
304572
Description:
single nucleotide variant
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NM_000401.3(EXT2):c.110C>T (p.Ser37Leu)

Allele ID
326466
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 44107723 (GRCh38) GRCh38 UCSC
11: 44129273 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.44107723C>T
NC_000011.9:g.44129273C>T
NM_000401.3:c.110C>T NP_000392.3:p.Ser37Leu missense
... more HGVS
Protein change
S37L, S4L
Other names
-
Canonical SPDI
NC_000011.10:44107722:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00006
Links
ClinGen: CA5954803
OMIM: 608210.0009
dbSNP: rs527624522
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000371317.2
Likely pathogenic 2 criteria provided, single submitter Jul 7, 2018 RCV000663343.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EXT2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
319 343

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jul 07, 2018)
criteria provided, single submitter
Method: research
Seizures, scoliosis, and macrocephaly syndrome
(Autosomal recessive inheritance)
Allele origin: inherited
Marseille Medical Genetics, U1251,Aix Marseille University, Inserm
Accession: SCV000783102.1
Submitted: (Jul 12, 2018)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple exostoses type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000371823.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Pathogenic
(Nov 06, 2020)
no assertion criteria provided
Method: literature only
SEIZURES, SCOLIOSIS, AND MICROCEPHALY SYNDROME
Allele origin: germline
OMIM
Accession: SCV000930612.2
Submitted: (Aug 02, 2019)
Evidence details
Publications
El-Bazzal, L., Atkinson, A.,  (more...)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
El-Bazzal, L., Atkinson, A., Gillart, A.-C., Obeid, M., Delague, V., Megarbane, A. A novel EXT2 mutation in a consanguineous family with severe developmental delay, microcephaly, seizures, feeding difficulties, and osteopenia extends the phenotypic spectrum of autosomal recessive EXT2-related syndrome (AREXT2). Europ. J. Med. Genet. 62: 259-264, 2019. - - - -

Text-mined citations for rs527624522...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021