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NC_000016.10:g.(?_30066878)_(30188984_?)del AND Severe combined immunodeficiency due to CORO1A deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 2, 2022
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:
RCV000815913.6

Allele description [Variation Report for NC_000016.10:g.(?_30066878)_(30188984_?)del]

NC_000016.10:g.(?_30066878)_(30188984_?)del

Genes:
  • LOC130058808:ATAC-STARR-seq lymphoblastoid active region 10688 [Gene]
  • LOC130058810:ATAC-STARR-seq lymphoblastoid active region 10689 [Gene]
  • LOC130058812:ATAC-STARR-seq lymphoblastoid active region 10690 [Gene]
  • LOC130058814:ATAC-STARR-seq lymphoblastoid active region 10691 [Gene]
  • LOC130058815:ATAC-STARR-seq lymphoblastoid active region 10692 [Gene]
  • LOC130058816:ATAC-STARR-seq lymphoblastoid active region 10693 [Gene]
  • LOC130058819:ATAC-STARR-seq lymphoblastoid active region 10695 [Gene]
  • LOC130058809:ATAC-STARR-seq lymphoblastoid silent region 7351 [Gene]
  • LOC130058811:ATAC-STARR-seq lymphoblastoid silent region 7352 [Gene]
  • LOC130058813:ATAC-STARR-seq lymphoblastoid silent region 7356 [Gene]
  • LOC130058817:ATAC-STARR-seq lymphoblastoid silent region 7357 [Gene]
  • LOC130058818:ATAC-STARR-seq lymphoblastoid silent region 7358 [Gene]
  • CORO1A-AS1:CORO1A antisense RNA 1 [Gene - HGNC]
  • LOC121587541:Sharpr-MPRA regulatory region 7413 [Gene]
  • LOC125146441:Sharpr-MPRA regulatory region 9068 [Gene]
  • TBX6:T-box transcription factor 6 [Gene - OMIM - HGNC]
  • YPEL3-DT:YPEL3 divergent transcript [Gene - HGNC]
  • ALDOA:aldolase, fructose-bisphosphate A [Gene - OMIM - HGNC]
  • CORO1A:coronin 1A [Gene - OMIM - HGNC]
  • GDPD3:glycerophosphodiester phosphodiesterase domain containing 3 [Gene - OMIM - HGNC]
  • MAPK3:mitogen-activated protein kinase 3 [Gene - OMIM - HGNC]
  • PPP4C:protein phosphatase 4 catalytic subunit [Gene - OMIM - HGNC]
  • LOC112694756:uncharaterized LOC112694756 [Gene]
  • YPEL3:yippee like 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p11.2
Genomic location:
Preferred name:
NC_000016.10:g.(?_30066878)_(30188984_?)del
HGVS:
  • NC_000016.10:g.(?_30066878)_(30188984_?)del
  • NC_000016.9:g.(?_30078199)_(30200305_?)del

Condition(s)

Name:
Severe combined immunodeficiency due to CORO1A deficiency
Synonyms:
Immunodeficiency 8; IMMUNODEFICIENCY 8 WITH LYMPHOPROLIFERATION
Identifiers:
MONDO: MONDO:0014168; MedGen: C3809383; Orphanet: 228003; OMIM: 615401

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000956392Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 2, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

The actin regulator coronin 1A is mutant in a thymic egress-deficient mouse strain and in a patient with severe combined immunodeficiency.

Shiow LR, Roadcap DW, Paris K, Watson SR, Grigorova IL, Lebet T, An J, Xu Y, Jenne CN, Föger N, Sorensen RU, Goodnow CC, Bear JE, Puck JM, Cyster JG.

Nat Immunol. 2008 Nov;9(11):1307-15. doi: 10.1038/ni.1662. Epub 2008 Oct 5.

PubMed [citation]
PMID:
18836449
PMCID:
PMC2672406

Compound heterozygous CORO1A mutations in siblings with a mucocutaneous-immunodeficiency syndrome of epidermodysplasia verruciformis-HPV, molluscum contagiosum and granulomatous tuberculoid leprosy.

Stray-Pedersen A, Jouanguy E, Crequer A, Bertuch AA, Brown BS, Jhangiani SN, Muzny DM, Gambin T, Sorte H, Sasa G, Metry D, Campbell J, Sockrider MM, Dishop MK, Scollard DM, Gibbs RA, Mace EM, Orange JS, Lupski JR, Casanova JL, Noroski LM.

J Clin Immunol. 2014 Oct;34(7):871-90. doi: 10.1007/s10875-014-0074-8. Epub 2014 Jul 30.

PubMed [citation]
PMID:
25073507
PMCID:
PMC4386834
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000956392.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. A similar copy number variant has been observed in individual(s) with T‚àíB+NK+ severe combined immunodeficiency (SCID) (PMID: 18836449). A gross deletion of the genomic region encompassing the full coding sequence of the CORO1A gene has been identified. Loss-of-function variants in CORO1A are known to be pathogenic (PMID: 18836449, 25073507). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Sep 29, 2024