SKA2 p.Gln23Gln

Variant names:

• chr17-59131331-A-A
• NM_182620.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr17-59131332--
• chr17-59131332-T-C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_182620.4(SKA2):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SKA2 NM_182620.4 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 0 publications found

Genes affected

SKA2 (HGNC:28006): (spindle and kinetochore associated complex subunit 2) Enables microtubule binding activity. Involved in several processes, including chromosome segregation; mitotic cell cycle; and regulation of microtubule polymerization or depolymerization. Located in spindle microtubule. Part of outer kinetochore. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182620.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SKA2	NM_182620.4	MANE Select	c.		exon_region	Exon 2 of 4	NP_872426.1	Q8WVK7-1
	SKA2	NM_001330399.2		c.		exon_region	Exon 2 of 4	NP_001317328.1	J3KSP0
	SKA2	NM_001100595.2		c.		exon_region	Exon 2 of 3	NP_001094065.1	Q8WVK7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SKA2	ENST00000330137.12	TSL:1 MANE Select	c.		exon_region	Exon 2 of 4	ENSP00000333433.7	Q8WVK7-1
	SKA2	ENST00000916133.1		c.		exon_region	Exon 2 of 4	ENSP00000586192.1
	SKA2	ENST00000583380.5	TSL:5	c.		exon_region	Exon 2 of 4	ENSP00000462574.1	J3KSP0

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.0

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.

Other links and lift over

hg19: chr17-57208692;