KLF8 p.Gln154Gln

Variant names:

• chrX-56265557-C-C
• NM_007250.5:c.

Your query was ambiguous. Multiple possible variants found:

• chrX-56265558--
• chrX-56265560-G-A

Variant summary

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

The NM_007250.5(KLF8):​c. variant causes a intron change. 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: 23)
• Consequence: KLF8 NM_007250.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.81
• Publications: 0 publications found

Genes affected

KLF8 (HGNC:6351): (KLF transcription factor 8) This gene encodes a protein which is a member of the Sp/KLF family of transcription factors. Members of this family contain a C-terminal DNA-binding domain with three Kruppel-like zinc fingers. The encoded protein is thought to play an important role in the regulation of epithelial to mesenchymal transition, a process which occurs normally during development but also during metastasis. A pseudogene has been identified on chromosome 16. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

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_007250.5. 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
	KLF8	NM_007250.5	MANE Select	c.		intron	N/A	NP_009181.2	O95600-1
	KLF8	NM_001324104.1		c.		intron	N/A	NP_001311033.1
	KLF8	NM_001324102.1		c.		intron	N/A	NP_001311031.1	O95600-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF8	ENST00000468660.6	TSL:1 MANE Select	c.		splice_donor intron	N/A	ENSP00000417303.1	O95600-1
	KLF8	ENST00000640927.1	TSL:1	c.		splice_donor intron	N/A	ENSP00000492126.1	O95600-4
	KLF8	ENST00000358094.7	TSL:1	n.		splice_donor intron	N/A	ENSP00000431911.1	Q05BZ3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.8

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: chrX-56291990;