NM_017780.4(CHD7):c.1797del (p.Lys601fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 31, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000489678.1

Allele description [Variation Report for NM_017780.4(CHD7):c.1797del (p.Lys601fs)]

NM_017780.4(CHD7):c.1797del (p.Lys601fs)

Genes:

LOC126860403:CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:61693034-61694233 [Gene]
CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q12.2

Genomic location:

Preferred name:

NM_017780.4(CHD7):c.1797del (p.Lys601fs)

HGVS:

NC_000008.11:g.60781131del
NG_007009.1:g.107352del
NM_001316690.1:c.1716+81del
NM_017780.4:c.1797delMANE SELECT
NP_060250.2:p.Lys601fs
LRG_176t1:c.1797del
LRG_176:g.107352del
NC_000008.10:g.61693690del
NM_017780.2:c.1797delG

Protein change:

K601fs

Links:

dbSNP: rs1085307830

NCBI 1000 Genomes Browser:

rs1085307830

Molecular consequence:

NM_017780.4:c.1797del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001316690.1:c.1716+81del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000577396	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 31, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000577396

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 31, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000577396.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1797delG variant in the CHD7 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. It is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The c.1797delG variant causes a frameshift starting with codon Lysine 601, changes this amino acid to a Arginine residue, and creates a premature Stop codon at position7 of the new reading frame, denoted p.Lys601ArgfsX7. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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