NC_000002.11:g.(?_166744769)_(166747518_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 17, 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:: RCV003122713.4

Allele description [Variation Report for NC_000002.11:g.(?_166744769)_(166747518_?)del]

NC_000002.11:g.(?_166744769)_(166747518_?)del

Gene:: TTC21B:tetratricopeptide repeat domain 21B [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 2q24.3
Genomic location:: Chr2: 166744769 - 166747518 (on Assembly GRCh37)
Preferred name:: NC_000002.11:g.(?_166744769)_(166747518_?)del
HGVS:: NC_000002.11:g.(?_166744769)_(166747518_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Jeune thoracic dystrophy (ATD1)
Synonyms:: Jeune syndrome; Infantile thoracic dystrophy; Thoracic pelvic phalangeal dystrophy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018770; MedGen: C0265275; OMIM: PS208500

Name:: Nephronophthisis
Synonyms:: juvenile nephronophthisis
Identifiers:: MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

Recent activity

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MULTISPECIES: dihydroorotase [Bacteroidota]
MULTISPECIES: dihydroorotase [Bacteroidota]
gi|1057224776|ref|WP_068597163.1|

Protein
MULTISPECIES: hypothetical protein [Bacteroidota]
MULTISPECIES: hypothetical protein [Bacteroidota]
gi|639237062|ref|WP_024567745.1|

Protein
MAG TPA: serine/threonine protein phosphatase [Bacteroidales bacterium]
MAG TPA: serine/threonine protein phosphatase [Bacteroidales bacterium]
tpg|HBX52577.1||gnl|WGS:DOSB|DEH02_

Protein
Chain A, 30kLP
Chain A, 30kLP
gi|310689717|pdb|3K8J|A

Protein
environmental samples 16S ribosomal RNA gene, partial sequence.
environmental samples 16S ribosomal RNA gene, partial sequence.
PopSet: 7767430

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003795558	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 17, 2022)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 18327258, 21068128, 21258341, 23559409, 24876116, 25492405, 27491411, 29068549, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003795558

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 17, 2022)

germline

clinical testing

PubMed (9)
[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

THM1 negatively modulates mouse sonic hedgehog signal transduction and affects retrograde intraflagellar transport in cilia.

Tran PV, Haycraft CJ, Besschetnova TY, Turbe-Doan A, Stottmann RW, Herron BJ, Chesebro AL, Qiu H, Scherz PJ, Shah JV, Yoder BK, Beier DR.

Nat Genet. 2008 Apr;40(4):403-410. doi: 10.1038/ng.105. Epub 2008 Mar 9.

PubMed [citation]

PMID:: 18327258
PMCID:: PMC4817720

Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy.

Otto EA, Ramaswami G, Janssen S, Chaki M, Allen SJ, Zhou W, Airik R, Hurd TW, Ghosh AK, Wolf MT, Hoppe B, Neuhaus TJ, Bockenhauer D, Milford DV, Soliman NA, Antignac C, Saunier S, Johnson CA, Hildebrandt F; GPN Study Group..

J Med Genet. 2011 Feb;48(2):105-16. doi: 10.1136/jmg.2010.082552. Epub 2010 Nov 10. Erratum in: J Med Genet. 2015 Dec;52(12):866. doi: 10.1136/jmg-2010-082552corr1.

PubMed [citation]

PMID:: 21068128
PMCID:: PMC3913043

See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003795558.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 23-25 of the TTC21B 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 TTC21B are known to be pathogenic (PMID: 18327258, 21068128, 21258341, 23559409, 24876116, 25492405, 27491411, 29068549). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TTC21B-related conditions.

#	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: Sep 29, 2024

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