Variant rs1554996989 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_ModeratePP5

The ENST00000686198.1(ENSG00000255320):n.294_407+103del variant causes a splice donor, splice donor 5th base, non coding transcript exon, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

ENST00000686198.1 splice_donor, splice_donor_5th_base, non_coding_transcript_exon, intron

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 1.11

Variant links:

Genes affected

(HGNC:):

links:

KLC2 (HGNC:20716): (kinesin light chain 2) The protein encoded by this gene is a light chain of kinesin, a molecular motor responsible for moving vesicles and organelles along microtubules. Defects in this gene are a cause of spastic paraplegia, optic atrophy, and neuropathy (SPOAN) syndrome. [provided by RefSeq, Mar 2016]

KLC2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PVS1

Splicing variant, NOT destroyed by nmd, known LOF gene.

PP5

Variant 11-66257085-AGCTAGGGCTGTGGATGAGCACTGCAGGAAGGCACTTCGGGGTCTATCAGAGGAAATTTTTGCTAACCTTCCGAGTTGTCTCAGAGCCAAACGTAGTAAGCTACCTGTCACCGGATGTGCTTGAGCTAAGGGCGCTGAACCACCTCTGTCAGAGACGGTGCATCCCCCACCGGATGTGACCCCGGGATGCGGAGCCTGGGGTCAGATCTGCGAGCCAG-A is Pathogenic according to our data. Variant chr11-66257085-AGCTAGGGCTGTGGATGAGCACTGCAGGAAGGCACTTCGGGGTCTATCAGAGGAAATTTTTGCTAACCTTCCGAGTTGTCTCAGAGCCAAACGTAGTAAGCTACCTGTCACCGGATGTGCTTGAGCTAAGGGCGCTGAACCACCTCTGTCAGAGACGGTGCATCCCCCACCGGATGTGACCCCGGGATGCGGAGCCTGGGGTCAGATCTGCGAGCCAG-A is described in ClinVar as [Pathogenic]. Clinvar id is 222029.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr11-66257085-AGCTAGGGCTGTGGATGAGCACTGCAGGAAGGCACTTCGGGGTCTATCAGAGGAAATTTTTGCTAACCTTCCGAGTTGTCTCAGAGCCAAACGTAGTAAGCTACCTGTCACCGGATGTGCTTGAGCTAAGGGCGCTGAACCACCTCTGTCAGAGACGGTGCATCCCCCACCGGATGTGACCCCGGGATGCGGAGCCTGGGGTCAGATCTGCGAGCCAG-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC124902694	XR_007062737.1 linkuse as main transcript	n.268+18_268+234del	intron_variant, non_coding_transcript_variant
KLC2	NM_001134775.2 linkuse as main transcript		5_prime_UTR_variant	1/16
KLC2	XM_047427414.1 linkuse as main transcript	c.-48-1461_-48-1245del	intron_variant
LOC124902694	XM_047427981.1 linkuse as main transcript	c.50+191_50+407del	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Appris	UniProt
	ENST00000686198.1 linkuse as main transcript	n.294_407+103del	splice_donor_variant, splice_donor_5th_base_variant, non_coding_transcript_exon_variant, intron_variant	1/3
KLC2	ENST00000417856.5 linkuse as main transcript		5_prime_UTR_variant	1/16	5	P1	Q9H0B6-1
KLC2	ENST00000531240.5 linkuse as main transcript		5_prime_UTR_variant	1/3	4

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Spastic paraplegia, optic atropy, and neuropathy

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 31, 2014

- -

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.