chr10-121520161-GCG-AGA

Variant names:

• chr10-121520161-GCG-AGA
• rs281865420
• NM_000141.5:c.755_757delCGCinsTCT

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP2 PP3 PP5

The NM_000141.5(FGFR2):​c.755_757delCGCinsTCT​(p.SerPro252PheSer) variant causes a missense 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 (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FGFR2 NM_000141.5 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.99

Genes affected

FGFR2 (HGNC:3689): (fibroblast growth factor receptor 2) The protein encoded by this gene is a member of the fibroblast growth factor receptor 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 is a high-affinity receptor for acidic, basic and/or keratinocyte growth factor, depending on the isoform. Mutations in this gene are associated with Crouzon syndrome, Pfeiffer syndrome, Craniosynostosis, Apert syndrome, Jackson-Weiss syndrome, Beare-Stevenson cutis gyrata syndrome, Saethre-Chotzen syndrome, and syndromic craniosynostosis. Multiple alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the FGFR2 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 114 curated pathogenic missense variants (we use a threshold of 10). The gene has 24 curated benign missense variants. Gene score misZ: 2.402 (below the threshold of 3.09). Trascript score misZ: 4.4365 (above the threshold of 3.09). GenCC associations: The gene is linked to Pfeiffer syndrome type 3, Antley-Bixler syndrome, Pfeiffer syndrome type 2, Saethre-Chotzen syndrome, Beare-Stevenson cutis gyrata syndrome, Crouzon syndrome, Jackson-Weiss syndrome, Pfeiffer syndrome type 1, LADD syndrome 1, Pfeiffer syndrome, bent bone dysplasia syndrome 1, Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis, familial scaphocephaly syndrome, McGillivray type, Apert syndrome, LADD syndrome.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 10-121520161-GCG-AGA is Pathogenic according to our data. Variant chr10-121520161-GCG-AGA is described in ClinVar as [Pathogenic]. Clinvar id is 13280.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFR2	NM_000141.5	c.755_757delCGCinsTCT	p.SerPro252PheSer	missense_variant		ENST00000358487.10	NP_000132.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFR2	ENST00000358487.10	c.755_757delCGCinsTCT	p.SerPro252PheSer	missense_variant		1	NM_000141.5	ENSP00000351276.6
FGFR2	ENST00000457416.7	c.755_757delCGCinsTCT	p.SerPro252PheSer	missense_variant		1		ENSP00000410294.2
FGFR2	ENST00000369056.5	c.755_757delCGCinsTCT	p.SerPro252PheSer	missense_variant		1		ENSP00000358052.1
FGFR2	ENST00000369058.7	c.755_757delCGCinsTCT	p.SerPro252PheSer	missense_variant		1		ENSP00000358054.3
FGFR2	ENST00000613048.4	c.488_490delCGCinsTCT	p.SerPro163PheSer	missense_variant		5		ENSP00000484154.1
FGFR2	ENST00000369059.5	c.410_412delCGCinsTCT	p.SerPro137PheSer	missense_variant		5		ENSP00000358055.1
FGFR2	ENST00000360144.7	c.488_490delCGCinsTCT	p.SerPro163PheSer	missense_variant		2		ENSP00000353262.3
FGFR2	ENST00000478859.5	c.71_73delCGCinsTCT	p.SerPro24PheSer	missense_variant		1		ENSP00000474011.1
FGFR2	ENST00000369061.8	c.749-4844_749-4842delCGCinsTCT		intron_variant	Intron 5 of 14	1		ENSP00000358057.4
FGFR2	ENST00000604236.5	n.410_412delCGCinsTCT		non_coding_transcript_exon_variant	Exon 5 of 17	1		ENSP00000474109.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Pfeiffer syndrome variant Pathogenic:1

Jan 01, 1997

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281865420; hg19: chr10-123279675;