NM_173354.5(SIK1):c.2083G>C (p.Ala695Pro) AND Developmental and epileptic encephalopathy, 30

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003751467.2

Allele description [Variation Report for NM_173354.5(SIK1):c.2083G>C (p.Ala695Pro)]

NM_173354.5(SIK1):c.2083G>C (p.Ala695Pro)

Gene:

SIK1:salt inducible kinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_173354.5(SIK1):c.2083G>C (p.Ala695Pro)

HGVS:

NC_000021.9:g.43417011C>G
NG_052009.1:g.15122G>C
NM_173354.5:c.2083G>CMANE SELECT
NP_775490.2:p.Ala695Pro
NC_000021.8:g.44836891C>G

Protein change:

A695P

Molecular consequence:

NM_173354.5:c.2083G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 30 (DEE30)
Synonyms:: Epileptic encephalopathy, early infantile, 30
Identifiers:: MONDO: MONDO:0014595; MedGen: C4225360; OMIM: 616341

Recent activity

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golgin subfamily A member 6-like protein 24, partial [Danio rerio]
golgin subfamily A member 6-like protein 24, partial [Danio rerio]
gi|2800568279|ref|XP_021324213.2|

Protein
golgin subfamily A member 6-like protein 25 [Danio rerio]
golgin subfamily A member 6-like protein 25 [Danio rerio]
gi|2800568285|ref|XP_068071828.1|

Protein
PREDICTED: Homo sapiens non-compact myelin associated protein (NCMAP), transcrip...
PREDICTED: Homo sapiens non-compact myelin associated protein (NCMAP), transcript variant X1, mRNA
gi|2217267401|ref|XM_011541463.3|

Nucleotide
sigma-54 dependent transcriptional regulator [Pseudomonas protegens]
sigma-54 dependent transcriptional regulator [Pseudomonas protegens]
gi|505447529|ref|WP_015634631.1|

Protein
PREDICTED: Benincasa hispida single-stranded DNA-binding protein, mitochondrial-...
PREDICTED: Benincasa hispida single-stranded DNA-binding protein, mitochondrial-like (LOC120083794), transcript variant X1, mRNA
gi|1955875335|ref|XM_039039670.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004549407	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004549407

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004549407.1

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 695 of the SIK1 protein (p.Ala695Pro). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SIK1-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SIK1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

Last Updated: Sep 29, 2024

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