11-64304830-CGTGACCTTCATTCGGTCACCGCA-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA

Variant names:

• chr11-64304830-C-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA
• rs3217060
• NM_001039496.2:c.*184_*185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA

Variant summary

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

The NM_001039496.2(CATSPERZ):​c.*184_*185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 150,184 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, 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: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CATSPERZ NM_001039496.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.922
• Publications: 1 publications found

Genes affected

CATSPERZ (HGNC:19231): (catsper channel auxiliary subunit zeta) Predicted to be involved in flagellated sperm motility; male meiotic nuclear division; and sperm capacitation. Located in cytoplasm and sperm principal piece. [provided by Alliance of Genome Resources, Apr 2022]

KCNK4-CATSPERZ (HGNC:56753): (KCNK4-CATSPERZ readthrough (NMD candidate)) This locus represents naturally occurring readthrough transcription between the neighboring KCNK4 (potassium channel subfamily K member 4) and the downstream TEX40 (testis expressed 40) chromosome 11. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Nov 2015]

ESRRA (HGNC:3471): (estrogen related receptor alpha) The protein encoded by this gene is a nuclear receptor that is most closely related to the estrogen receptor. This protein acts as a site-specific transcription factor and interacts with members of the PGC-1 family of transcription cofactors to regulate the expression of most genes involved in cellular energy production as well as in the process of mitochondrial biogenesis. A processed pseudogene of ESRRA is located on chromosome 13q12.1. [provided by RefSeq, Jun 2019]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039496.2. 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
	CATSPERZ	NM_001039496.2	MANE Select	c.*184_*185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		downstream_gene	N/A	NP_001034585.1	Q9NTU4
	KCNK4-CATSPERZ	NR_133662.1		n.*61_*62insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CATSPERZ	ENST00000328404.8	TSL:1 MANE Select	c.*184_*185insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		downstream_gene	N/A	ENSP00000491717.1	Q9NTU4
	KCNK4-CATSPERZ	ENST00000539086.5	TSL:1	n.*61_*62insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		downstream_gene	N/A
	ESRRA	ENST00000965463.1		c.-344_-343insGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA		upstream_gene	N/A	ENSP00000635522.1

Frequencies

GnomAD3 genomes AF: 0.0000200 AC: 3 AN: 150068 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000488

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 394654 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 207804

African (AFR) AF: 0.00 AC: 0 AN: 11380

American (AMR) AF: 0.00 AC: 0 AN: 15642

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11824

East Asian (EAS) AF: 0.00 AC: 0 AN: 26970

South Asian (SAS) AF: 0.00 AC: 0 AN: 38606

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25926

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1872

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 239422

Other (OTH) AF: 0.00 AC: 0 AN: 23012

GnomAD4 genome AF: 0.0000200 AC: 3 AN: 150184 Hom.: 0 Cov.: 32 AF XY: 0.0000273 AC XY: 2 AN XY: 73368

African (AFR) AF: 0.0000487 AC: 2 AN: 41088

American (AMR) AF: 0.00 AC: 0 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3432

East Asian (EAS) AF: 0.00 AC: 0 AN: 5060

South Asian (SAS) AF: 0.00 AC: 0 AN: 4712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10442

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000149 AC: 1 AN: 67006

Other (OTH) AF: 0.00 AC: 0 AN: 2090

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.92

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

dbSNP: rs3217060;

hg19: chr11-64072302;