rs1060499663

Positions:

• chr8-38416012-TC-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_023110.3(FGFR1):​c.1711delG​(p.Glu571fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: FGFR1 NM_023110.3 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.91

Genes affected

FGFR1 (HGNC:3688): (fibroblast growth factor receptor 1) The protein encoded by this gene is a member of the fibroblast growth factor receptor (FGFR) family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member binds both acidic and basic fibroblast growth factors and is involved in limb induction. Mutations in this gene have been associated with Pfeiffer syndrome, Jackson-Weiss syndrome, Antley-Bixler syndrome, osteoglophonic dysplasia, and autosomal dominant Kallmann syndrome 2. Chromosomal aberrations involving this gene are associated with stem cell myeloproliferative disorder and stem cell leukemia lymphoma syndrome. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

FGFR1 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 8-38416012-TC-T is Pathogenic according to our data. Variant chr8-38416012-TC-T is described in ClinVar as [Pathogenic]. Clinvar id is 397530.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFR1	NM_023110.3	c.1711delG	p.Glu571fs	frameshift_variant	13/18	ENST00000447712.7	NP_075598.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR1	ENST00000447712.7	c.1711delG	p.Glu571fs	frameshift_variant	13/18	1	NM_023110.3	ENSP00000400162.2
FGFR1	ENST00000397091.9	c.1705delG	p.Glu569fs	frameshift_variant	13/18	1		ENSP00000380280.5
FGFR1	ENST00000397108.8	c.1705delG	p.Glu569fs	frameshift_variant	14/19	1		ENSP00000380297.4
FGFR1	ENST00000397113.6	c.1705delG	p.Glu569fs	frameshift_variant	13/18	2		ENSP00000380302.2
FGFR1	ENST00000356207.9	c.1444delG	p.Glu482fs	frameshift_variant	12/17	1		ENSP00000348537.5
FGFR1	ENST00000397103.5	c.1444delG	p.Glu482fs	frameshift_variant	11/16	5		ENSP00000380292.1
FGFR1	ENST00000326324.10	c.1438delG	p.Glu480fs	frameshift_variant	12/17	1		ENSP00000327229.6
FGFR1	ENST00000487647.5	n.*1402delG		non_coding_transcript_exon_variant	12/12	1		ENSP00000435254.1
FGFR1	ENST00000487647.5	n.*1402delG		3_prime_UTR_variant	12/12	1		ENSP00000435254.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypogonadotropic hypogonadism 2 with or without anosmia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center of Genomic medicine, Geneva, University Hospital of Geneva

Oct 13, 2014

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1060499663; hg19: chr8-38273530;