NM_001379081.2(FREM1):c.346A>G (p.Thr116Ala) AND not provided

Germline classification:: Uncertain significance (1 submission)
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:: RCV004720196.1

Allele description [Variation Report for NM_001379081.2(FREM1):c.346A>G (p.Thr116Ala)]

NM_001379081.2(FREM1):c.346A>G (p.Thr116Ala)

Gene:

FREM1:FRAS1 related extracellular matrix 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p22.3

Genomic location:

Preferred name:

NM_001379081.2(FREM1):c.346A>G (p.Thr116Ala)

HGVS:

NC_000009.12:g.14859468T>C
NG_017005.2:g.55769A>G
NM_001370060.1:c.346A>G
NM_001370063.1:c.346A>G
NM_001370065.1:c.346A>G
NM_001379081.2:c.346A>GMANE SELECT
NM_144966.5:c.346A>G
NM_144966.7:c.346A>G
NP_001356989.1:p.Thr116Ala
NP_001356992.1:p.Thr116Ala
NP_001356994.1:p.Thr116Ala
NP_001366010.1:p.Thr116Ala
NP_659403.4:p.Thr116Ala
NC_000009.11:g.14859466T>C
NR_163238.2:n.1162A>G
NR_163239.2:n.920A>G
NR_163240.1:n.1157A>G
NR_163241.1:n.1157A>G

Protein change:

T116A

Molecular consequence:

NM_001370060.1:c.346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370063.1:c.346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001370065.1:c.346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379081.2:c.346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_144966.7:c.346A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_163238.2:n.1162A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_163239.2:n.920A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_163240.1:n.1157A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_163241.1:n.1157A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV005326334	Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV005326334

Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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

Citations

PubMed

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 Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital, SCV005326334.1

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

Description

A variant of uncertain clinical significance was identified in the FREM1 gene. This variant is absent from the medical literature, patient databases, and large population studies (gnomAD v2.1.1). Notably, two other variants at the same amino acid position (p.Thr116Ser and p.Thr116Ile) are present in large population studies at very low frequencies. The p.Thr116Ser variant is also present in a patient database (ClinVar Variation ID: 1520000). Computational tools have conflicting predictions about the possible impact of the p.Thr116Ala change on protein function.

#	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 8, 2024

ClinVar

Relating variation to medicine