12-48918750-GTA-G

Variant names:

• chr12-48918750-GTA-G
• rs863223325
• NM_033124.5:c.877_878delAT

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PVS1 PP5_Very_Strong

The NM_033124.5(DRC2):​c.877_878delAT​(p.Ile293ProfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. I293I) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.00015 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: DRC2 NM_033124.5 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 0.239
• Publications: 3 publications found

Genes affected

DRC2 (HGNC:29937): (coiled-coil domain containing 65) This gene encodes a sperm tail protein that is highly expressed in adult testis, spermatocytes and spermatids. The protein plays a critical role in the assembly of the nexin-dynein regulatory complex. Mutations in this gene result in primary ciliary dyskinesia. [provided by RefSeq, Nov 2013]

DRC2 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 27

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000272822 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 16 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 12-48918750-GTA-G is Pathogenic according to our data. Variant chr12-48918750-GTA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 88685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRC2	NM_033124.5	c.877_878delAT	p.Ile293ProfsTer2	frameshift_variant	Exon 6 of 8	ENST00000320516.5	NP_149115.2
DRC2	NM_001286957.2	c.448_449delAT	p.Ile150ProfsTer2	frameshift_variant	Exon 6 of 8		NP_001273886.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC65	ENST00000320516.5	c.877_878delAT	p.Ile293ProfsTer2	frameshift_variant	Exon 6 of 8	1	NM_033124.5	ENSP00000312706.4
ENSG00000272822	ENST00000398092.4	c.385-14844_385-14843delTA		intron_variant	Intron 4 of 4	3		ENSP00000438507.1

Frequencies

GnomAD3 genomes AF: 0.000151 AC: 23 AN: 152144 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000203 AC: 51 AN: 251484 AF XY: 0.000199

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00427

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000703

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000130 AC: 190 AN: 1461862 Hom.: 0 AF XY: 0.000135 AC XY: 98 AN XY: 727230

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 113 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5742

European-Non Finnish (NFE) AF: 0.0000486 AC: 54 AN: 1112012

Other (OTH) AF: 0.000381 AC: 23 AN: 60390

GnomAD4 genome AF: 0.000151 AC: 23 AN: 152144 Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8 AN XY: 74328

African (AFR) AF: 0.00 AC: 0 AN: 41422

American (AMR) AF: 0.00 AC: 0 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 68026

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

Alfa AF: 0.000136 Hom.: 0

Bravo AF: 0.000151

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Primary ciliary dyskinesia 27 Pathogenic:4

Dec 23, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Ile293Profs*2) in the CCDC65 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CCDC65 are known to be pathogenic (PMID: 23991085, 24094744). This variant is present in population databases (rs748630203, gnomAD 0.4%). This premature translational stop signal has been observed in individual(s) with primary ciliary dyskinesia (PMID: 23991085, 24094744). It is commonly reported in individuals of Ashkenazi Jewish ancestry (PMID: 23991085, 24094744). This variant is also known as 876_877delAT. ClinVar contains an entry for this variant (Variation ID: 88685). For these reasons, this variant has been classified as Pathogenic. -

Oct 03, 2013

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Dec 17, 2021

Johns Hopkins Genomics, Johns Hopkins University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CCDC65 c.877_878del has been reported in the homozygous state in multiple individuals with primary ciliary dyskinesia. This variant (rs1272967209) has an entry in ClinVar and has been identified in a large population dataset. The minor allele frequency is neither low enough to consider the variant rare (<0.1%) nor high enough to consider it a population polymorphism (>1%) within the Ashkenazi Jewish subpopulation (gnomAD: 45/10370 alleles; 0.4339%, no homozygotes). This frameshift variant results in a premature stop codon in exon 6 of 8 likely leading to nonsense-mediated decay and lack of protein production. We consider CCDC65 c.877_878del to be pathogenic. -

Apr 24, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

not provided Pathogenic:2

Jun 30, 2023

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; This variant is associated with the following publications: (PMID: 24094744, 23991085, 34693619) -

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia Pathogenic:1

Nov 30, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Ile293fs variant in CCDC65 has been previously reported in 3 Ashkenazi Jew ish individuals with primary ciliary dyskinesia (PCD) and segregated with diseas e in 1 affected family member (Austin-Tse 2013, Horani 2013). All of these indiv iduals were homozygous for the variant. This variant has also been identified in 20/66728 European chromosomes by the Exome Aggregation Consortium (ExAC, http:/ /exac.broadinstitute.org) and in 0.14% (3/2070) of chromosomes from an Ashkenazi Jewish control cohort (Fedick 2015). Although this variant has been seen in the general population, its frequency is still low enough to be consistent with a r ecessive carrier frequency. The p.Ile293fs variant is predicted to cause a frame shift, which alters the protein?s amino acid sequence beginning at position 293 and leads to a premature termination codon 2 amino acids downstream. This altera tion is then predicted to lead to a truncated or absent protein. In vitro studie s have demonstrated that the CCDC65 protein was absent in cells derived from an individual homozygous for this variant (Horani 2013). Functional studies in huma n cell lines and the zebrafish model provided some evidence that loss of functio n of the CCDC65 gene may cause cilia motility defects (Horani 2013, Austin-Tse 2 013), though these types of assays may not accurately reflect biological functio n. The p.Ile293fs variant is currently the only variant in CCDC65 gene that has been reported in individuals with PCD, therefore additional studies are needed t o fully understand the role of the CCDC65 gene in disease. In summary, although additional studies are required to fully establish its clinical significance, th e p.Ile293fs variant is likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs863223325; hg19: chr12-49312533;