CZIB p.Ser123Ser

Variant names:

• chr1-53216026-C-C
• NM_017887.3:c.

Your query was ambiguous. Multiple possible variants found:

• chr1-53216027--
• chr1-53216027-T-A
• chr1-53216027-T-G
• chr1-53216027-T-C
• chr1-53216027-TGA-ACT
• chr1-53216027-TGA-GCT

Variant summary

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

The NM_017887.3(CZIB):​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: CZIB NM_017887.3 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 0 publications found

Genes affected

CZIB (HGNC:26059): (CXXC motif containing zinc binding protein) Enables zinc ion binding activity. [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_017887.3. 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
	CZIB	NM_017887.3	MANE Select	c.		exon_region	Exon 7 of 8	NP_060357.1	Q9NWV4
	CZIB	NM_001304759.2		c.		exon_region	Exon 6 of 7	NP_001291688.1
	CZIB	NM_001304760.2		c.		exon_region	Exon 5 of 6	NP_001291689.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CZIB	ENST00000294360.5	TSL:1 MANE Select	c.		exon_region	Exon 7 of 8	ENSP00000294360.4	Q9NWV4
	CZIB	ENST00000470385.5	TSL:1	n.		exon_region	Exon 6 of 7
	CZIB	ENST00000912019.1		c.		exon_region	Exon 6 of 7	ENSP00000582078.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.5

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: chr1-53681698;