NM_001048166.1(STIL):c.1136C>T (p.Ser379Phe) AND Microcephaly 7, primary, autosomal recessive

Germline classification:: Uncertain significance (4 submissions)
Last evaluated:: May 23, 2017
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:: RCV000147679.12

Allele description [Variation Report for NM_001048166.1(STIL):c.1136C>T (p.Ser379Phe)]

NM_001048166.1(STIL):c.1136C>T (p.Ser379Phe)

Gene:

STIL:STIL centriolar assembly protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p33

Genomic location:

Preferred name:

NM_001048166.1(STIL):c.1136C>T (p.Ser379Phe)

HGVS:

NC_000001.11:g.47282457G>A
NG_012126.1:g.36691C>T
NM_001048166.1:c.1136C>TMANE SELECT
NM_001282936.1:c.1136C>T
NM_001282937.1:c.1136C>T
NM_001282938.1:c.995C>T
NM_001282939.1:c.995C>T
NM_003035.2:c.1136C>T
NP_001041631.1:p.Ser379Phe
NP_001269865.1:p.Ser379Phe
NP_001269866.1:p.Ser379Phe
NP_001269867.1:p.Ser332Phe
NP_001269868.1:p.Ser332Phe
NP_003026.2:p.Ser379Phe
NC_000001.10:g.47748129G>A

Protein change:

S332F

Links:

dbSNP: rs149185431

NCBI 1000 Genomes Browser:

rs149185431

Molecular consequence:

NM_001048166.1:c.1136C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001282936.1:c.1136C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001282937.1:c.1136C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001282938.1:c.995C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001282939.1:c.995C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003035.2:c.1136C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Microcephaly 7, primary, autosomal recessive
Identifiers:: MONDO: MONDO:0012989; MedGen: C2675187; Orphanet: 2512; OMIM: 612703

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000195130	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Uncertain significance (Dec 28, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000611524	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 23, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001254501	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV003931228	GenomeConnect - Brain Gene Registry	no classification provided	not provided	unknown	phenotyping only

Help

Summary from all submissions

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

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

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 Genetic Services Laboratory, University of Chicago, SCV000195130.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV000611524.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV001254501.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown 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

From GenomeConnect - Brain Gene Registry, SCV003931228.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	phenotyping only	not provided

Description

Variant classified as Uncertain significance and reported on 12-06-2016 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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

Last Updated: Oct 20, 2024

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