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NC_000006.11:g.(?_3083299)_(3106305_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 30, 2023
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:
RCV004578816.2

Allele description [Variation Report for NC_000006.11:g.(?_3083299)_(3106305_?)del]

NC_000006.11:g.(?_3083299)_(3106305_?)del

Gene:
RIPK1:receptor interacting serine/threonine kinase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6p25.2
Genomic location:
Chr6: 3083299 - 3106305 (on Assembly GRCh37)
Preferred name:
NC_000006.11:g.(?_3083299)_(3106305_?)del
HGVS:
NC_000006.11:g.(?_3083299)_(3106305_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005067554Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 30, 2023) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Primary immunodeficiency with chronic enteropathy and developmental delay in a boy arising from a novel homozygous RIPK1 variant.

Uchiyama Y, Kim CA, Pastorino AC, Ceroni J, Lima PP, de Barros Dorna M, Honjo RS, Bertola D, Hamanaka K, Fujita A, Mitsuhashi S, Miyatake S, Takata A, Miyake N, Mizuguchi T, Matsumoto N.

J Hum Genet. 2019 Sep;64(9):955-960. doi: 10.1038/s10038-019-0631-3. Epub 2019 Jun 18.

PubMed [citation]
PMID:
31213653

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005067554.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 5-9 of the RIPK1 gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in RIPK1 are known to be pathogenic (PMID: 31213653). This variant has not been reported in the literature in individuals affected with RIPK1-related conditions. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024