NM_001048166.1(STIL):c.3754A>G (p.Ile1252Val) AND Microcephaly 7, primary, autosomal recessive

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 1, 2020
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:: RCV001101741.6

Allele description [Variation Report for NM_001048166.1(STIL):c.3754A>G (p.Ile1252Val)]

NM_001048166.1(STIL):c.3754A>G (p.Ile1252Val)

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.3754A>G (p.Ile1252Val)

HGVS:

NC_000001.11:g.47251249T>C
NG_012126.1:g.67899A>G
NM_001048166.1:c.3754A>GMANE SELECT
NM_001282936.1:c.3751A>G
NM_001282937.1:c.3700A>G
NM_001282938.1:c.3613A>G
NM_001282939.1:c.3559A>G
NM_003035.2:c.3751A>G
NP_001041631.1:p.Ile1252Val
NP_001269865.1:p.Ile1251Val
NP_001269866.1:p.Ile1234Val
NP_001269867.1:p.Ile1205Val
NP_001269868.1:p.Ile1187Val
NP_003026.2:p.Ile1251Val
NC_000001.10:g.47716921T>C

Protein change:

I1187V

Links:

dbSNP: rs142210835

NCBI 1000 Genomes Browser:

rs142210835

Molecular consequence:

NM_001048166.1:c.3754A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282936.1:c.3751A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282937.1:c.3700A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282938.1:c.3613A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282939.1:c.3559A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003035.2:c.3751A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001258378	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001520310	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 1, 2020)	unknown	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

SCV001258378

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV001520310

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 1, 2020)

unknown

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

Citations

PubMed

In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ).

Kumar A, Rajendran V, Sethumadhavan R, Purohit R.

FEBS Open Bio. 2012 Sep 25;2:285-93. doi: 10.1016/j.fob.2012.09.003. Print 2012.

PubMed [citation]

PMID:: 23772360
PMCID:: PMC3678130

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 Illumina Laboratory Services, Illumina, SCV001258378.1

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

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). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant 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 Baylor Genetics, SCV001520310.1

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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

Last Updated: Apr 9, 2023

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