chr1-245688125-CGGGACCTCGCCCCCCAGCTCCG-C

Position:

• chr1-245688125-CGGGACCTCGCCCCCCAGCTCCG-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_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
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 4.00

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]

LOC105373265 (HGNC:):

ACMG classification

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
KIF26B	NM_018012.4	c.5146_5167delACCTCGCCCCCCAGCTCCGGGG	p.Thr1716fs	frameshift_variant	12/15	ENST00000407071.7	NP_060482.2
LOC105373265	XR_007066988.1	n.657-3696_657-3675delCGGAGCTGGGGGGCGAGGTCCC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.5146_5167delACCTCGCCCCCCAGCTCCGGGG	p.Thr1716fs	frameshift_variant	12/15	1	NM_018012.4	ENSP00000385545.2
KIF26B	ENST00000366518.4	c.4003_4024delACCTCGCCCCCCAGCTCCGGGG	p.Thr1335fs	frameshift_variant	9/12	5		ENSP00000355475.4

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

Submissions by phenotype

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Division of Blood Purification, Kakanzawa University’

Oct 19, 2015

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886037758; hg19: chr1-245851427;