17-81208979-CT-GA

Variant names:

• chr17-81208979-CT-GA
• NM_014984.4:c.220_221delAGinsTC
• CEP131 p.Arg74Ser

Variant summary

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

The NM_014984.4(CEP131):​c.220_221delAGinsTC​(p.Arg74Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CEP131 NM_014984.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.78
• Publications: 0 publications found

Genes affected

CEP131 (HGNC:29511): (centrosomal protein 131) Enables protein homodimerization activity. Involved in several processes, including intraciliary transport involved in cilium assembly; protein localization to centrosome; and regulation of centrosome duplication. Located in several cellular components, including ciliary transition zone; intercellular bridge; and microtubule organizing center. Colocalizes with centrosome. [provided by Alliance of Genome Resources, Apr 2022]

CEP131 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014984.4. 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
	CEP131	NM_014984.4	MANE Select	c.220_221delAGinsTC	p.Arg74Ser	missense	N/A	NP_055799.2	Q9UPN4-2
	CEP131	NM_001319228.2		c.220_221delAGinsTC	p.Arg74Ser	missense	N/A	NP_001306157.1	Q9UPN4-1
	CEP131	NM_001319229.2		c.220_221delAGinsTC	p.Arg74Ser	missense	N/A	NP_001306158.1	I3L2J8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP131	ENST00000450824.7	TSL:1 MANE Select	c.220_221delAGinsTC	p.Arg74Ser	missense	N/A	ENSP00000393583.2	Q9UPN4-2
	CEP131	ENST00000269392.8	TSL:1	c.220_221delAGinsTC	p.Arg74Ser	missense	N/A	ENSP00000269392.4	Q9UPN4-1
	CEP131	ENST00000575907.5	TSL:1	c.220_221delAGinsTC	p.Arg74Ser	missense	N/A	ENSP00000459733.1	I3L2J8

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.8

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: chr17-79182779;