NM_023110.3(FGFR1):c.1671del (p.Leu557fs) AND Encephalocraniocutaneous lipomatosis

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 1, 2016
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:: RCV001199033.2

Allele description [Variation Report for NM_023110.3(FGFR1):c.1671del (p.Leu557fs)]

NM_023110.3(FGFR1):c.1671del (p.Leu557fs)

Gene:

FGFR1:fibroblast growth factor receptor 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8p11.23

Genomic location:

Preferred name:

NM_023110.3(FGFR1):c.1671del (p.Leu557fs)

HGVS:

NC_000008.11:g.38416053del
NG_007729.1:g.57782del
NM_001174063.2:c.1665del
NM_001174064.2:c.1641del
NM_001174065.2:c.1665del
NM_001174066.2:c.1404del
NM_001174067.2:c.1764del
NM_001354367.2:c.1665del
NM_001354368.2:c.1392del
NM_001354369.2:c.1659del
NM_001354370.2:c.1398del
NM_015850.4:c.1665del
NM_023105.3:c.1404del
NM_023106.3:c.1398del
NM_023110.3:c.1671delMANE SELECT
NP_001167534.1:p.Leu555fs
NP_001167535.1:p.Leu547fs
NP_001167536.1:p.Leu555fs
NP_001167537.1:p.Leu468fs
NP_001167538.1:p.Leu588fs
NP_001341296.1:p.Leu555fs
NP_001341297.1:p.Leu464fs
NP_001341298.1:p.Leu553fs
NP_001341299.1:p.Leu466fs
NP_056934.2:p.Leu555fs
NP_075593.1:p.Leu468fs
NP_075594.1:p.Leu466fs
NP_075598.2:p.Leu557fs
LRG_993:g.57782del
NC_000008.10:g.38273571del
NM_001174067.1:c.1764delG

Protein change:

L464fs

Links:

dbSNP: rs1816433701

NCBI 1000 Genomes Browser:

rs1816433701

Molecular consequence:

NM_001174063.2:c.1665del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174064.2:c.1641del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174065.2:c.1665del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174066.2:c.1404del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174067.2:c.1764del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354367.2:c.1665del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354368.2:c.1392del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354369.2:c.1659del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354370.2:c.1398del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015850.4:c.1665del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023105.3:c.1404del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023106.3:c.1398del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_023110.3:c.1671del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Encephalocraniocutaneous lipomatosis (ECCL)
Identifiers:: MONDO: MONDO:0013074; MedGen: C0406612; Orphanet: 2396; OMIM: 613001

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001370028	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 1, 2016)	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

SCV001370028

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 1, 2016)

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	unknown	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 Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001370028.2

#	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 classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP4.

#	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: Dec 17, 2022

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