chr11-65888042-T-TTTA

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP3PP5

The NM_004214.5(FIBP):​c.175_176insTAA​(p.His59delinsLeuAsn) variant causes a protein altering 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: 32)

Consequence

FIBP
NM_004214.5 protein_altering

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 8.71
Variant links:
Genes affected
FIBP (HGNC:3705): (FGF1 intracellular binding protein) Acidic fibroblast growth factor is mitogenic for a variety of different cell types and acts by stimulating mitogenesis or inducing morphological changes and differentiation. The FIBP protein is an intracellular protein that binds selectively to acidic fibroblast growth factor (aFGF). It is postulated that FIBP may be involved in the mitogenic action of aFGF. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_004214.5. Strenght limited to Supporting due to length of the change: 1aa.
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
Variant 11-65888042-T-TTTA is Pathogenic according to our data. Variant chr11-65888042-T-TTTA is described in ClinVar as [Pathogenic]. Clinvar id is 254242.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FIBPNM_004214.5 linkuse as main transcriptc.175_176insTAA p.His59delinsLeuAsn protein_altering_variant 2/10 ENST00000357519.9
FIBPNM_198897.2 linkuse as main transcriptc.175_176insTAA p.His59delinsLeuAsn protein_altering_variant 2/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FIBPENST00000357519.9 linkuse as main transcriptc.175_176insTAA p.His59delinsLeuAsn protein_altering_variant 2/101 NM_004214.5 P4O43427-2

Frequencies

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

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Tall stature-intellectual disability-renal anomalies syndrome Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMSep 15, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs886037928; hg19: chr11-65655513; API