Single allele AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 28, 2024
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:: RCV003494599.1

Allele description [Variation Report for Single allele]

Genes:

ABI3:ABI family member 3 [Gene - OMIM - HGNC]
ABCC3:ATP binding cassette subfamily C member 3 [Gene - OMIM - HGNC]
ATP5MC1:ATP synthase membrane subunit c locus 1 [Gene - OMIM - HGNC]
GNGT2:G protein subunit gamma transducin 2 [Gene - OMIM - HGNC]
LUC7L3:LUC7 like 3 pre-mRNA splicing factor [Gene - OMIM - HGNC]
MYCBPAP:MYCBP associated protein [Gene - OMIM - HGNC]
PRAC1:PRAC1 small nuclear protein [Gene - OMIM - HGNC]
PRAC2:PRAC2 small nuclear protein [Gene - OMIM - HGNC]
SNF8:SNF8 subunit of ESCRT-II [Gene - OMIM - HGNC]
ACSF2:acyl-CoA synthetase family member 2 [Gene - OMIM - HGNC]
ANKRD40:ankyrin repeat domain 40 [Gene - HGNC]
B4GALNT2:beta-1,4-N-acetyl-galactosaminyltransferase 2 (SID blood group) [Gene - OMIM - HGNC]
CALCOCO2:calcium binding and coiled-coil domain 2 [Gene - OMIM - HGNC]
CACNA1G:calcium voltage-gated channel subunit alpha1 G [Gene - OMIM - HGNC]
CHAD:chondroadherin [Gene - OMIM - HGNC]
COL1A1:collagen type I alpha 1 chain [Gene - OMIM - HGNC]
DLX3:distal-less homeobox 3 [Gene - OMIM - HGNC]
DLX4:distal-less homeobox 4 [Gene - OMIM - HGNC]
EPN3:epsin 3 [Gene - OMIM - HGNC]
EME1:essential meiotic structure-specific endonuclease 1 [Gene - OMIM - HGNC]
FAM117A:family with sequence similarity 117 member A [Gene - HGNC]
GIP:gastric inhibitory polypeptide [Gene - OMIM - HGNC]
HOXB13:homeobox B13 [Gene - OMIM - HGNC]
IGF2BP1:insulin like growth factor 2 mRNA binding protein 1 [Gene - OMIM - HGNC]
ITGA3:integrin subunit alpha 3 [Gene - OMIM - HGNC]
LRRC59:leucine rich repeat containing 59 [Gene - OMIM - HGNC]
KAT7:lysine acetyltransferase 7 [Gene - OMIM - HGNC]
MRPL27:mitochondrial ribosomal protein L27 [Gene - OMIM - HGNC]
NGFR:nerve growth factor receptor [Gene - OMIM - HGNC]
NXPH3:neurexophilin 3 [Gene - OMIM - HGNC]
PHOSPHO1:phosphoethanolamine/phosphocholine phosphatase 1 [Gene - HGNC]
PHB1:prohibitin 1 [Gene - OMIM - HGNC]
PPP1R9B:protein phosphatase 1 regulatory subunit 9B [Gene - OMIM - HGNC]
PDK2:pyruvate dehydrogenase kinase 2 [Gene - OMIM - HGNC]
RSAD1:radical S-adenosyl methionine domain containing 1 [Gene - OMIM - HGNC]
SGCA:sarcoglycan alpha [Gene - OMIM - HGNC]
SLC35B1:solute carrier family 35 member B1 [Gene - OMIM - HGNC]
SPOP:speckle type BTB/POZ protein [Gene - OMIM - HGNC]
SPATA20:spermatogenesis associated 20 [Gene - OMIM - HGNC]
SAMD14:sterile alpha motif domain containing 14 [Gene - OMIM - HGNC]
TRQ-TTG1-1:tRNA-Gln (anticodon TTG) 1-1 [Gene - OMIM - HGNC]
TAC4:tachykinin precursor 4 [Gene - OMIM - HGNC]
TMEM92:transmembrane protein 92 [Gene - OMIM - HGNC]
TTLL6:tubulin tyrosine ligase like 6 [Gene - OMIM - HGNC]
UBE2Z:ubiquitin conjugating enzyme E2 Z [Gene - OMIM - HGNC]
XYLT2:xylosyltransferase 2 [Gene - OMIM - HGNC]
ZNF652:zinc finger protein 652 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q21.32-21.33

Genomic location:

Chr17: 46740736 - 48853218 (on Assembly GRCh37)

Observations:

Condition(s)

Name:: Tricho-dento-osseous syndrome (TDO)
Synonyms:: TDO syndrome; Enamel hypoplasia and hypocalcification with associated strikingly curly hair
Identifiers:: MONDO: MONDO:0008592; MedGen: C0265333; Orphanet: 3352; OMIM: 190320

Name:: Osteogenesis imperfecta type I (OI1)
Synonyms:: OI, TYPE I; Osteogenesis imperfecta type 1; OI type 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008146; MedGen: C0023931; Orphanet: 666; OMIM: 166200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004232721	Rare Disease Group, Clinical Genetics, Karolinska Institutet	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 28, 2024)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004232721

Rare Disease Group, Clinical Genetics, Karolinska Institutet

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 28, 2024)

de novo

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Rare Disease Group, Clinical Genetics, Karolinska Institutet, SCV004232721.1

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

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

Last Updated: Feb 20, 2024

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