VCV001027565.1 - ClinVar

NM_001384140.1(PCDH15):c.3667_3668del (p.Ile1223fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001384140.1(PCDH15):c.3667_3668del (p.Ile1223fs)

Variation ID: 1027565 Accession: VCV001027565.1

Type and length

Deletion, 2 bp

Location

Cytogenetic: 10q21.1 10: 53866691-53866692 (GRCh38) [ NCBI UCSC ] 10: 55626451-55626452 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 19, 2021	Mar 19, 2021	Oct 1, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NM_001384140.1:c.3667_3668del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001371069.1:p.Ile1223fs	frameshift
NM_033056.4:c.3667_3668del MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_149045.3:p.Ile1223fs	frameshift
NM_033056.4:c.3667_3668delAT MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_001142763.2:c.3682_3683del	NP_001136235.1:p.Ile1228fs	frameshift
NM_001142764.2:c.3667_3668del	NP_001136236.1:p.Ile1223fs	frameshift
NM_001142765.2:c.3454_3455del	NP_001136237.1:p.Ile1152fs	frameshift
NM_001142766.2:c.3667_3668del	NP_001136238.1:p.Ile1223fs	frameshift
NM_001142767.2:c.3556_3557del	NP_001136239.1:p.Ile1186fs	frameshift
NM_001142768.2:c.3601_3602del	NP_001136240.1:p.Ile1201fs	frameshift
NM_001142769.3:c.3703_3704del	NP_001136241.1:p.Ile1235fs	frameshift
NM_001142770.3:c.3667_3668del	NP_001136242.1:p.Ile1223fs	frameshift
NM_001142771.2:c.3682_3683del	NP_001136243.1:p.Ile1228fs	frameshift
NM_001142772.2:c.3667_3668del	NP_001136244.1:p.Ile1223fs	frameshift
NM_001142773.2:c.3601_3602del	NP_001136245.1:p.Ile1201fs	frameshift
NM_001354404.2:c.3601_3602del	NP_001341333.1:p.Ile1201fs	frameshift
NM_001354411.2:c.3688_3689del	NP_001341340.1:p.Ile1230fs	frameshift
NM_001354420.2:c.3667_3668del	NP_001341349.1:p.Ile1223fs	frameshift
NM_001354429.2:c.3667_3668del	NP_001341358.1:p.Ile1223fs	frameshift
NC_000010.11:g.53866692_53866693del
NC_000010.10:g.55626452_55626453del
NG_009191.3:g.1767491_1767492del

... more HGVS ... less HGVS

Protein change

I1152fs, I1186fs, I1201fs, I1223fs, I1228fs, I1230fs, I1235fs

Other names

Canonical SPDI

NC_000010.11:53866690:ATA:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

dbSNP: rs2079481708 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PCDH15		-	-	GRCh38 GRCh37	3395	3485

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Autosomal recessive nonsyndromic hearing loss 23 Usher syndrome type 1D Usher syndrome type 1F	Pathogenic (1)	no assertion criteria provided	Oct 1, 2020	RCV001328030.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Oct 01, 2020)	no assertion criteria provided Method: research	Autosomal recessive nonsyndromic hearing loss 23 Usher syndrome type 1D Usher syndrome type 1F This variant is in the PCDH15 gene (more...) (Autosomal recessive inheritance) Affected status: yes Allele origin: germline, paternal	National Institute on Deafness and Communication Disorders, National Institutes of Health Accession: SCV001519363.1 First in ClinVar: Mar 19, 2021 Last updated: Mar 19, 2021 Comment: was found associated in trans with NM_033056.4:c.1737C>G	Observation 1: Clinical Features: Profound childhood hearing loss (present) Family history: yes Age: 10-19 years Sex: male Ethnicity/Population group: African,Yoruba Geographic origin: Nigeria;Ibadan Segregation observed: yes Secondary finding: no Method: Verified by Sanger sequencing Observation 2: Clinical Features: Profound childhood hearing loss (present) Family history: yes Age: 10-19 years Sex: male Ethnicity/Population group: African,Yoruba Geographic origin: Nigeria;Ibadan Segregation observed: yes Secondary finding: no Method: Verified by Sanger sequencing Observation 3: Clinical Features: Profound childhood hearing loss (present) Family history: yes Age: 0-9 years Sex: female Ethnicity/Population group: African,Yoruba Geographic origin: Nigeria;Ibadan Segregation observed: yes Secondary finding: no Method: Verified by Sanger sequencing Observation 4: Clinical Features: Profound childhood hearing loss (present) Family history: yes Age: 0-9 years Sex: female Ethnicity/Population group: African,Yoruba Geographic origin: Nigeria;Ibadan Segregation observed: yes Secondary finding: no Method: Verified by Sanger sequencing Observation 5: Clinical Features: Profound childhood hearing loss (present) Family history: yes Age: 0-9 years Sex: female Ethnicity/Population group: African,Yoruba Geographic origin: Nigeria;Ibadan Segregation observed: yes Secondary finding: no Method: Verified by Sanger sequencing Observation 6: Clinical Features: Profound childhood hearing loss (present) Family history: yes Age: 0-9 years Sex: female Ethnicity/Population group: African,Yoruba Geographic origin: Nigeria;Ibadan Segregation observed: yes Secondary finding: no Method: Verified by Sanger sequencing

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs2079481708 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 08, 2024

ClinVar Genomic variation as it relates to human health

NM_001384140.1(PCDH15):c.3667_3668del (p.Ile1223fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs2079481708 ...