NC_000009.11:g.(?_116917341)_(116918270_?)del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 4, 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:: RCV003122915.2

Allele description

NC_000009.11:g.(?_116917341)_(116918270_?)del

Gene:: COL27A1:collagen type XXVII alpha 1 chain [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 9q32
Genomic location:: Chr9: 116917341 - 116918270 (on Assembly GRCh37)
Preferred name:: NC_000009.11:g.(?_116917341)_(116918270_?)del
HGVS:: NC_000009.11:g.(?_116917341)_(116918270_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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Chromatin binding by HORMAD proteins regulates meiotic recombination initiation
Chromatin binding by HORMAD proteins regulates meiotic recombination initiation
Chromatin binding by HORMAD proteins regulates meiotic recombination initiation

BioProject
Melanophryniscus sp. Morro Boa Vista isolate MBoaVista6 tRNA-Met gene, partial s...
Melanophryniscus sp. Morro Boa Vista isolate MBoaVista6 tRNA-Met gene, partial sequence; NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala, and tRNA-Asn genes, complete sequence; and tRNA-Cys gene, partial sequence; mitochondrial
gi|1042074714|gb|KX025755.1|

Nucleotide
Melanophryniscus sp. Morro Boa Vista isolate MBoaVista2 tRNA-Met gene, partial s...
Melanophryniscus sp. Morro Boa Vista isolate MBoaVista2 tRNA-Met gene, partial sequence; NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala, and tRNA-Asn genes, complete sequence; and tRNA-Cys gene, partial sequence; mitochondrial
gi|1042074706|gb|KX025751.1|

Nucleotide
Streptococcus pyogenes strain S47 superoxide dismutase (sodA) gene, partial cds
Streptococcus pyogenes strain S47 superoxide dismutase (sodA) gene, partial cds
gi|1928139077|gb|MT560929.1|

Nucleotide
uncharacterized protein PgNI_01733 [Pyricularia grisea]
uncharacterized protein PgNI_01733 [Pyricularia grisea]
gi|1758257445|ref|XP_030985979.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003795781	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 4, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24986830, 28276056, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003795781

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 4, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population.

Gonzaga-Jauregui C, Gamble CN, Yuan B, Penney S, Jhangiani S, Muzny DM, Gibbs RA, Lupski JR, Hecht JT.

Eur J Hum Genet. 2015 Mar;23(3):342-6. doi: 10.1038/ejhg.2014.107. Epub 2014 Jul 2.

PubMed [citation]

PMID:: 24986830
PMCID:: PMC4326704

Second family provides further evidence for causation of Steel syndrome by biallelic mutations in COL27A1.

Kotabagi S, Shah H, Shukla A, Girisha KM.

Clin Genet. 2017 Sep;92(3):323-326. doi: 10.1111/cge.13006. Epub 2017 Apr 19.

PubMed [citation]

PMID:: 28276056

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003795781.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant results in the deletion of part of exon 1 (c.-890_41del) of the COL27A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL27A1 are known to be pathogenic (PMID: 24986830, 28276056). This variant has not been reported in the literature in individuals affected with COL27A1-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 18, 2023

ClinVar

Relating variation to medicine