chr10-84211698-T-A

Variant names:

• chr10-84211698-T-A
• rs786205459
• NM_033100.4:c.1536T>A

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_033100.4(CDHR1):​c.1536T>A​(p.Tyr512*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CDHR1 NM_033100.4 stop_gained
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.0120
• Publications: 1 publications found

Genes affected

CDHR1 (HGNC:14550): (cadherin related family member 1) This gene belongs to the cadherin superfamily of calcium-dependent cell adhesion molecules. The encoded protein is a photoreceptor-specific cadherin that plays a role in outer segment disc morphogenesis. Mutations in this gene are associated with inherited retinal dystrophies. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2013]

CDHR1 Gene-Disease associations (from GenCC):

• cone-rod dystrophy 15

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• cone-rod dystrophy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 10-84211698-T-A is Pathogenic according to our data. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-84211698-T-A is described in CliVar as Likely_pathogenic. Clinvar id is 191005.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR1	NM_033100.4	c.1536T>A	p.Tyr512*	stop_gained	Exon 14 of 17	ENST00000623527.4	NP_149091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR1	ENST00000623527.4	c.1536T>A	p.Tyr512*	stop_gained	Exon 14 of 17	1	NM_033100.4	ENSP00000485478.1
CDHR1	ENST00000332904.7	c.1536T>A	p.Tyr512*	stop_gained	Exon 14 of 17	1		ENSP00000331063.3
CDHR1	ENST00000372117.6	c.750T>A	p.Tyr250*	stop_gained	Exon 7 of 10	2		ENSP00000361189.4
CDHR1	ENST00000622973.1	n.267T>A		non_coding_transcript_exon_variant	Exon 3 of 6	5		ENSP00000485151.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

-

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	36
DANN	Uncertain	0.98
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.62
FATHMM_MKL	Uncertain	0.96	D
PhyloP100		0.012
Vest4		0.52
GERP RS		-4.0
Mutation Taster		=2/198	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs786205459; hg19: chr10-85971454;