chr10-92649986-G-T

Position:

• chr10-92649986-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2 PP3_Strong PP5_Moderate

The NM_004523.4(KIF11):​c.2922G>T​(p.Pro974=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P974P) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KIF11 NM_004523.4 splice_region, synonymous
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.08

Genes affected

KIF11 (HGNC:6388): (kinesin family member 11) This gene encodes a motor protein that belongs to the kinesin-like protein family. Members of this protein family are known to be involved in various kinds of spindle dynamics. The function of this gene product includes chromosome positioning, centrosome separation and establishing a bipolar spindle during cell mitosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 10-92649986-G-T is Pathogenic according to our data. Variant chr10-92649986-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 1064447.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF11	NM_004523.4	c.2922G>T	p.Pro974=	splice_region_variant, synonymous_variant	20/22	ENST00000260731.5	NP_004514.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000260731.5	c.2922G>T	p.Pro974=	splice_region_variant, synonymous_variant	20/22	1	NM_004523.4	ENSP00000260731	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Microcephaly Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing;in vitro

Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People’s Hospital

Nov 25, 2020

The c.2922G>T variant in KIF11 was a denovo variant, which has not been reported in HGMD and ClinVar database. While the same site variant c.2922G>A has been reported conflicting interpretations in pathogenicity of Microcephaly with or without chorioretinopathy, lymphedema, or mental retardation, the functional mechanism study was absence. In our study, we found this variant in a Children with microcephaly through Whole exonsequencing. Then we applied the minigene experiment to fristly identify that this variant result in the wrong splicing site of exon20 derived pre-mRNA, thus leading to the deletion of the whole or part of exon20 mRNA. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	20
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.92
SpliceAI score (max)		0.47		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.47		Position offset: 0

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: chr10-94409743;