chr10-121520016-T-C

Variant names:

• chr10-121520016-T-C
• rs1554930684
• NM_000141.5:c.902A>G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PM2 PP2 PP3

The NM_000141.5(FGFR2):​c.902A>G​(p.Tyr301Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FGFR2 NM_000141.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.68

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 Likely_pathogenic. Variant got 6 ACMG points.

• PM1: In a disulfide_bond (size 64) in uniprot entity FGFR2_HUMAN there are 35 pathogenic changes around while only 1 benign (97%) in NM_000141.5
• 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: MetaRNN computational evidence supports a deleterious effect, 0.784

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFR2	NM_000141.5	c.902A>G	p.Tyr301Cys	missense_variant	Exon 7 of 18	ENST00000358487.10	NP_000132.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFR2	ENST00000358487.10	c.902A>G	p.Tyr301Cys	missense_variant	Exon 7 of 18	1	NM_000141.5	ENSP00000351276.6
FGFR2	ENST00000457416.7	c.902A>G	p.Tyr301Cys	missense_variant	Exon 7 of 18	1		ENSP00000410294.2
FGFR2	ENST00000369056.5	c.902A>G	p.Tyr301Cys	missense_variant	Exon 6 of 17	1		ENSP00000358052.1
FGFR2	ENST00000369058.7	c.902A>G	p.Tyr301Cys	missense_variant	Exon 7 of 17	1		ENSP00000358054.3
FGFR2	ENST00000613048.4	c.635A>G	p.Tyr212Cys	missense_variant	Exon 6 of 17	5		ENSP00000484154.1
FGFR2	ENST00000369059.5	c.557A>G	p.Tyr186Cys	missense_variant	Exon 5 of 16	5		ENSP00000358055.1
FGFR2	ENST00000360144.7	c.635A>G	p.Tyr212Cys	missense_variant	Exon 6 of 17	2		ENSP00000353262.3
FGFR2	ENST00000478859.5	c.218A>G	p.Tyr73Cys	missense_variant	Exon 6 of 17	1		ENSP00000474011.1
FGFR2	ENST00000369061.8	c.749-4697A>G		intron_variant	Intron 5 of 14	1		ENSP00000358057.4
FGFR2	ENST00000604236.5	n.557A>G		non_coding_transcript_exon_variant	Exon 5 of 17	1		ENSP00000474109.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

FGFR2-related craniosynostosis Uncertain:1

Jul 03, 2016

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, this variant is a rare missense change with uncertain impact on protein function. While it is absent from the population and reported in affected individuals, the available evidence is currently insufficient to definitively determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces tyrosine with cysteine at codon 301 of the FGFR2 protein (p.Tyr301Cys). The tyrosine residue is moderately conserved and there is a large physicochemical difference between tyrosine and cysteine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in 2 individuals affected with Crouzon Syndrome (PMID: 9521581, 18391498). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
CADD	Uncertain	26
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.88	.;.;D;.;.;.;T;.;T;.;.;.;.;.
Eigen	Benign	0.067
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.91	D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.20	D
MetaRNN	Pathogenic	0.78	D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.62	D
MutationAssessor	Benign	1.2	.;.;L;.;.;L;.;L;.;L;.;L;L;.
PrimateAI	Pathogenic	0.81	D
PROVEAN	Pathogenic	-4.6	D;.;D;.;D;D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.72
Sift	Uncertain	0.023	D;.;D;.;D;T;D;D;D;D;D;D;D;D
Sift4G	Benign	0.11	T;T;T;T;T;T;T;T;T;T;T;T;T;.
Polyphen		0.0070	B;.;.;.;B;.;.;.;.;.;B;B;.;.
Vest4		0.80
MutPred		0.74		.;.;Gain of methylation at K300 (P = 0.0183);.;.;Gain of methylation at K300 (P = 0.0183);.;Gain of methylation at K300 (P = 0.0183);Gain of methylation at K300 (P = 0.0183);Gain of methylation at K300 (P = 0.0183);.;Gain of methylation at K300 (P = 0.0183);Gain of methylation at K300 (P = 0.0183);.;
MVP		0.98
MPC		1.6
ClinPred		0.91	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.36
gMVP		0.90

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: rs1554930684; hg19: chr10-123279530;