rs113994193

chr20-10431708-T-TCAGGCCGCCA

Variant summary

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

The ENST00000399054.6(MKKS):c.-674_-673insTGGCGGCCTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MKKS ENST00000399054.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

MKKS (HGNC:7108): (MKKS centrosomal shuttling protein) This gene encodes a protein which shares sequence similarity with other members of the type II chaperonin family. The encoded protein is a centrosome-shuttling protein and plays an important role in cytokinesis. This protein also interacts with other type II chaperonin members to form a complex known as the BBSome, which involves ciliary membrane biogenesis. This protein is encoded by a downstream open reading frame (dORF). Several upstream open reading frames (uORFs) have been identified, which repress the translation of the dORF, and two of which can encode small mitochondrial membrane proteins. Mutations in this gene have been observed in patients with Bardet-Biedl syndrome type 6, also known as McKusick-Kaufman syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2023]

LOC128706665 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC128706665	NM_001394148.2	c.-22+2399_-22+2400insTGGCGGCCTG		intron_variant		ENST00000649912.2
LOC128706666	NM_001394149.2	c.-276+2399_-276+2400insTGGCGGCCTG		intron_variant		ENST00000713549.1
MKKS	NM_170784.3	c.-649+2399_-649+2400insTGGCGGCCTG		intron_variant		ENST00000347364.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MKKS	ENST00000347364.7	c.-649+2399_-649+2400insTGGCGGCCTG		intron_variant		1	NM_170784.3	P1
	ENST00000649912.2	c.-22+2399_-22+2400insTGGCGGCCTG		intron_variant			NM_001394148.2	P1
	ENST00000713549.1	c.-276+2399_-276+2400insTGGCGGCCTG		intron_variant			NM_001394149.2	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

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: rs113994193; hg19: chr20-10412356;