5-44305170-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004465.2(FGF10):​c.452A>T​(p.Lys151Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

FGF10
NM_004465.2 missense

Scores

4
14
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.33
Variant links:
Genes affected
FGF10 (HGNC:3666): (fibroblast growth factor 10) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein exhibits mitogenic activity for keratinizing epidermal cells, but essentially no activity for fibroblasts, which is similar to the biological activity of FGF7. Studies of the mouse homolog of suggested that this gene is required for embryonic epidermal morphogenesis including brain development, lung morphogenesis, and initiation of lim bud formation. This gene is also implicated to be a primary factor in the process of wound healing. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FGF10NM_004465.2 linkc.452A>T p.Lys151Met missense_variant Exon 3 of 3 ENST00000264664.5 NP_004456.1 O15520A0A7U3JW18
FGF10XM_005248264.5 linkc.452A>T p.Lys151Met missense_variant Exon 4 of 4 XP_005248321.1 O15520A0A7U3JW18

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FGF10ENST00000264664.5 linkc.452A>T p.Lys151Met missense_variant Exon 3 of 3 1 NM_004465.2 ENSP00000264664.4 O15520

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Congenital absence of salivary gland;C5774287:Lacrimoauriculodentodigital syndrome 3 Uncertain:1
May 23, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Pathogenic
0.18
D
BayesDel_noAF
Uncertain
0.010
CADD
Pathogenic
27
DANN
Uncertain
0.99
DEOGEN2
Pathogenic
0.90
D
Eigen
Pathogenic
0.71
Eigen_PC
Pathogenic
0.69
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.94
D
M_CAP
Uncertain
0.092
D
MetaRNN
Uncertain
0.68
D
MetaSVM
Uncertain
0.78
D
MutationAssessor
Uncertain
2.4
M
PrimateAI
Uncertain
0.72
T
PROVEAN
Uncertain
-3.5
D
REVEL
Uncertain
0.63
Sift
Uncertain
0.0060
D
Sift4G
Uncertain
0.011
D
Polyphen
1.0
D
Vest4
0.47
MutPred
0.49
Loss of methylation at K151 (P = 0.0088);
MVP
0.88
MPC
2.9
ClinPred
0.98
D
GERP RS
5.9
Varity_R
0.52
gMVP
0.74

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-44305272; API