chr1-245688125-CGGGACCTCGCCCCCCAGCTCCG-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate

The NM_018012.4(KIF26B):​c.5146_5167delACCTCGCCCCCCAGCTCCGGGG​(p.Thr1716fs) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

KIF26B
NM_018012.4 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 4.00
Variant links:
Genes affected
KIF26B (HGNC:25484): (kinesin family member 26B) The protein encoded by this gene is an intracellular motor protein thought to transport organelles along microtubules. The encoded protein is required for kidney development. Elevated levels of this protein have been found in some breast and colorectal cancers. [provided by RefSeq, Mar 2017]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-245688125-CGGGACCTCGCCCCCCAGCTCCG-C is Pathogenic according to our data. Variant chr1-245688125-CGGGACCTCGCCCCCCAGCTCCG-C is described in ClinVar as [Pathogenic]. Clinvar id is 217290.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIF26BNM_018012.4 linkc.5146_5167delACCTCGCCCCCCAGCTCCGGGG p.Thr1716fs frameshift_variant 12/15 ENST00000407071.7 NP_060482.2 Q2KJY2-1
LOC105373265XR_007066988.1 linkn.657-3696_657-3675delCGGAGCTGGGGGGCGAGGTCCC intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIF26BENST00000407071.7 linkc.5146_5167delACCTCGCCCCCCAGCTCCGGGG p.Thr1716fs frameshift_variant 12/151 NM_018012.4 ENSP00000385545.2 Q2KJY2-1
KIF26BENST00000366518.4 linkc.4003_4024delACCTCGCCCCCCAGCTCCGGGG p.Thr1335fs frameshift_variant 9/125 ENSP00000355475.4 B7WPD9

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not provided Pathogenic:1
Pathogenic, criteria provided, single submitterresearchDivision of Blood Purification, Kakanzawa University’Oct 19, 2015- -

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: rs886037758; hg19: chr1-245851427; API