NC_000006.11:g.(?_35773448)_(36953949_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 12, 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:: RCV004578894.2

Allele description [Variation Report for NC_000006.11:g.(?_35773448)_(36953949_?)del]

NC_000006.11:g.(?_35773448)_(36953949_?)del

Genes:

BNIP5:BCL2 interacting protein 5 [Gene - HGNC]
ETV7:ETS variant transcription factor 7 [Gene - OMIM - HGNC]
LHFPL5:LHFPL tetraspan subfamily member 5 [Gene - OMIM - HGNC]
RAB44:RAB44, member RAS oncogene family [Gene - HGNC]
SRPK1:SRSF protein kinase 1 [Gene - OMIM - HGNC]
BRPF3:bromodomain and PHD finger containing 3 [Gene - OMIM - HGNC]
C6orf89:chromosome 6 open reading frame 89 [Gene - OMIM - HGNC]
CPNE5:copine 5 [Gene - OMIM - HGNC]
CDKN1A:cyclin dependent kinase inhibitor 1A [Gene - OMIM - HGNC]
MTCH1:mitochondrial carrier 1 [Gene - OMIM - HGNC]
MAPK13:mitogen-activated protein kinase 13 [Gene - OMIM - HGNC]
MAPK14:mitogen-activated protein kinase 14 [Gene - OMIM - HGNC]
PNPLA1:patatin like phospholipase domain containing 1 [Gene - OMIM - HGNC]
PI16:peptidase inhibitor 16 [Gene - HGNC]
PPIL1:peptidylprolyl isomerase like 1 [Gene - OMIM - HGNC]
PXT1:peroxisomal testis enriched protein 1 [Gene - HGNC]
KCTD20:potassium channel tetramerization domain containing 20 [Gene - OMIM - HGNC]
SRSF3:serine and arginine rich splicing factor 3 [Gene - OMIM - HGNC]
STK38:serine/threonine kinase 38 [Gene - OMIM - HGNC]
SLC26A8:solute carrier family 26 member 8 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p21.31-21.2

Genomic location:

Chr6: 35773448 - 36953949 (on Assembly GRCh37)

Preferred name:

NC_000006.11:g.(?_35773448)_(36953949_?)del

HGVS:

NC_000006.11:g.(?_35773448)_(36953949_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Neotoma floridana isolate NK64089 engrailed 2 (EN2) gene, exon 3 and partial cds
Neotoma floridana isolate NK64089 engrailed 2 (EN2) gene, exon 3 and partial cds
gi|77417458|gb|DQ180004.1|

Nucleotide
Neotoma stephensi isolate TK77928 engrailed 2 (EN2) gene, exon 3 and partial cds
Neotoma stephensi isolate TK77928 engrailed 2 (EN2) gene, exon 3 and partial cds
gi|77417454|gb|DQ180002.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005067632	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 12, 2023)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15905332, 16459341, 21816241, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005067632

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 12, 2023)

unknown

clinical testing

PubMed (4)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A missense mutation in the previously undescribed gene Tmhs underlies deafness in hurry-scurry (hscy) mice.

Longo-Guess CM, Gagnon LH, Cook SA, Wu J, Zheng QY, Johnson KR.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7894-9. Epub 2005 May 19.

PubMed [citation]

PMID:: 15905332
PMCID:: PMC1142366

Mutations of human TMHS cause recessively inherited non-syndromic hearing loss.

Shabbir MI, Ahmed ZM, Khan SY, Riazuddin S, Waryah AM, Khan SN, Camps RD, Ghosh M, Kabra M, Belyantseva IA, Friedman TB, Riazuddin S.

J Med Genet. 2006 Aug;43(8):634-40. Epub 2006 Feb 3.

PubMed [citation]

PMID:: 16459341
PMCID:: PMC2564584

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005067632.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with LHFPL5-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the LHFPL5 gene has been identified. Loss-of-function variants in LHFPL5 are known to be pathogenic (PMID: 15905332, 16459341, 21816241). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine