Genetic Variant FKBP7:p.Val112Leu (chr2-178477099-AAC-CAG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_181342.3(FKBP7):c.334_336delGTTinsCTG(p.Val112Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

FKBP7
NM_181342.3 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.64

Publications

0 publications found

Variant links:

Genes affected

FKBP7 (HGNC:3723): (FKBP prolyl isomerase 7) The protein encoded by this gene belongs to the FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) family. Members of this family exhibit PPIase activity and function as molecular chaperones. A similar protein in mouse is located in the endoplasmic reticulum and binds calcium. [provided by RefSeq, Jul 2008]

FKBP7 links:

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new If you want to explore the variant's impact on the transcript NM_181342.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181342.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FKBP7	NM_181342.3	MANE Select	c.334_336delGTTinsCTG	p.Val112Leu	missense	N/A	NP_851939.1	Q9Y680-2
FKBP7	NM_001135212.2		c.334_336delGTTinsCTG	p.Val112Leu	missense	N/A	NP_001128684.1	Q9Y680-3
FKBP7	NM_001410972.1		c.334_336delGTTinsCTG	p.Val112Leu	missense	N/A	NP_001397901.1	B4DRE2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FKBP7	ENST00000424785.7	TSL:1 MANE Select	c.334_336delGTTinsCTG	p.Val112Leu	missense	N/A	ENSP00000413152.2	Q9Y680-2
FKBP7	ENST00000434643.6	TSL:1	c.334_336delGTTinsCTG	p.Val112Leu	missense	N/A	ENSP00000415486.2	Q9Y680-3
FKBP7	ENST00000233092.10	TSL:1	n.334_336delGTTinsCTG		non_coding_transcript_exon	Exon 2 of 5	ENSP00000233092.6	Q9Y680-1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over