NM_198253.3(TERT):c.999CTC[1] (p.Ser335del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 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:: RCV002535868.9

Allele description [Variation Report for NM_198253.3(TERT):c.999CTC[1] (p.Ser335del)]

NM_198253.3(TERT):c.999CTC[1] (p.Ser335del)

Gene:

TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_198253.3(TERT):c.999CTC[1] (p.Ser335del)

Other names:

p.Ser335del

HGVS:

NC_000005.10:g.1293882GAG[1]
NC_000005.9:g.1293997_1293999del
NG_009265.1:g.6161CTC[1]
NM_001193376.3:c.999CTC[1]
NM_198253.3:c.999CTC[1]MANE SELECT
NP_001180305.1:p.Ser335del
NP_937983.2:p.Ser335del
LRG_343t1:c.1002_1004del
LRG_343:g.6161CTC[1]
NC_000005.9:g.1293997GAG[1]
NC_000005.9:g.1293997_1293999del
NC_000005.9:g.1293997_1293999delGAG
NM_198253.2:c.1002_1004del
NM_198253.2:c.1002_1004delCTC
NM_198253.3:c.1002_1004delCTCMANE SELECT
NR_149162.3:n.1078CTC[1]
NR_149163.3:n.1078CTC[1]

Protein change:

S335del

Links:

dbSNP: rs1170942980

NCBI 1000 Genomes Browser:

rs1170942980

Molecular consequence:

NM_001193376.3:c.999CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_198253.3:c.999CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_149162.3:n.1078CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.1078CTC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Dyskeratosis congenita, autosomal dominant 2
Identifiers:: MONDO: MONDO:0013521; MedGen: C3151443; OMIM: 613989

Name:: Idiopathic Pulmonary Fibrosis
Synonyms:: Idiopathic fibrosing alveolitis, chronic form
Identifiers:: MeSH: D054990; MedGen: C1800706

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000931528	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 12, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26329388, 28102861, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000931528

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 12, 2023)

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

Clinical and genetic features of dyskeratosis congenita, cryptic dyskeratosis congenita, and Hoyeraal-Hreidarsson syndrome in Japan.

Yamaguchi H, Sakaguchi H, Yoshida K, Yabe M, Yabe H, Okuno Y, Muramatsu H, Takahashi Y, Yui S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Inokuchi K, Ito E, Ogawa S, Kojima S.

Int J Hematol. 2015 Nov;102(5):544-52. doi: 10.1007/s12185-015-1861-6. Epub 2015 Sep 2.

PubMed [citation]

PMID:: 26329388

Clinical utility of next-generation sequencing for inherited bone marrow failure syndromes.

Muramatsu H, Okuno Y, Yoshida K, Shiraishi Y, Doisaki S, Narita A, Sakaguchi H, Kawashima N, Wang X, Xu Y, Chiba K, Tanaka H, Hama A, Sanada M, Takahashi Y, Kanno H, Yamaguchi H, Ohga S, Manabe A, Harigae H, Kunishima S, Ishii E, et al.

Genet Med. 2017 Jul;19(7):796-802. doi: 10.1038/gim.2016.197. Epub 2017 Jan 19.

PubMed [citation]

PMID:: 28102861

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000931528.6

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

Description

This variant, c.1002_1004del, results in the deletion of 1 amino acid(s) of the TERT protein (p.Ser335del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 639452). This variant has been observed in individual(s) with clinical features of dyskeratosis congenita (PMID: 26329388, 28102861).

#	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: May 1, 2024

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