11-64304830-CGTGACCTTCATTCGGTCACCGCA-CGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGCA

Variant names:

• chr11-64304852-C-CAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC
• NM_001039496.2:c.*206_*207insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC

Variant summary

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

The NM_001039496.2(CATSPERZ):​c.*206_*207insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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 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: not found (cov: 32)
• Consequence: CATSPERZ NM_001039496.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 0 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.*206_*207insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC		downstream_gene	N/A	NP_001034585.1	Q9NTU4
	KCNK4-CATSPERZ	NR_133662.1		n.*83_*84insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC		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.*206_*207insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC		downstream_gene	N/A	ENSP00000491717.1	Q9NTU4
	KCNK4-CATSPERZ	ENST00000539086.5	TSL:1	n.*83_*84insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC		downstream_gene	N/A
	ESRRA	ENST00000965463.1		c.-322_-321insAGTGACCTTCATTCGGTCACCGCAGTGACCTTCATTCGGTCACCGC		upstream_gene	N/A	ENSP00000635522.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.58

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: chr11-64072324;