NM_024753.5(TTC21B):c.2572C>T (p.Arg858Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 13, 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:: RCV001917908.4

Allele description [Variation Report for NM_024753.5(TTC21B):c.2572C>T (p.Arg858Ter)]

NM_024753.5(TTC21B):c.2572C>T (p.Arg858Ter)

Gene:

TTC21B:tetratricopeptide repeat domain 21B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_024753.5(TTC21B):c.2572C>T (p.Arg858Ter)

HGVS:

NC_000002.12:g.165901907G>A
NG_030345.1:g.56932C>T
NM_024753.5:c.2572C>TMANE SELECT
NP_079029.3:p.Arg858Ter
NC_000002.11:g.166758417G>A

Protein change:

R858*

Links:

dbSNP: rs895624584

NCBI 1000 Genomes Browser:

rs895624584

Molecular consequence:

NM_024753.5:c.2572C>T - nonsense - [Sequence Ontology: SO:0001587]

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

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Uncultured rumen bacterium jw20RRI 16S ribosomal RNA gene, partial sequence
Uncultured rumen bacterium jw20RRI 16S ribosomal RNA gene, partial sequence
gi|7767490|gb|AF218607.1|

Nucleotide
MAG TPA: hypothetical protein DEH02_16020 [Bacteroidales bacterium]
MAG TPA: hypothetical protein DEH02_16020 [Bacteroidales bacterium]
tpg|HBX52571.1||gnl|WGS:DOSB|DEH02_

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002170719	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 13, 2023)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 18327258, 21068128, 21258341, 23559409, 24876116, 25492405, 29068549, 27491411, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002170719

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 13, 2023)

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, SCV002170719.3

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

Description

This sequence change creates a premature translational stop signal (p.Arg858*) in the TTC21B gene. It is expected to 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). This variant is present in population databases (no rsID available, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with nephronophthisis-related ciliopathy (PMID: 27491411). ClinVar contains an entry for this variant (Variation ID: 1399888). 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: Sep 29, 2024

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