NM_015631.6(TCTN3):c.1224_1226del (p.Gln408_Gly409delinsHis) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 8, 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:: RCV003108910.4

Allele description [Variation Report for NM_015631.6(TCTN3):c.1224_1226del (p.Gln408_Gly409delinsHis)]

NM_015631.6(TCTN3):c.1224_1226del (p.Gln408_Gly409delinsHis)

Gene:

TCTN3:tectonic family member 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q24.1

Genomic location:

Preferred name:

NM_015631.6(TCTN3):c.1224_1226del (p.Gln408_Gly409delinsHis)

HGVS:

NC_000010.11:g.95683173_95683175del
NG_032953.1:g.15969_15971del
NM_001013840.1:c.1278_1280delGGG
NM_001143973.2:c.780_782del
NM_001410982.1:c.1128_1130delGGG
NM_015631.6:c.1224_1226delMANE SELECT
NP_001013862.1:p.Gln426_Gly427delinsHis
NP_001137445.1:p.Gln260_Gly261delinsHis
NP_001397911.1:p.Gln376_Gly377delinsHis
NP_056446.4:p.Gln408_Gly409delinsHis
NC_000010.10:g.97442930_97442932del

Molecular consequence:

NM_001013840.1:c.1278_1280delGGG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001143973.2:c.780_782del - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001410982.1:c.1128_1130delGGG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_015631.6:c.1224_1226del - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:: Orofacial-digital syndrome IV (OFD4)
Synonyms:: OFD SYNDROME, BARAITSER-BURN TYPE; OFDS IV; ORAL-FACIAL-DIGITAL SYNDROME, TYPE IV; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009794; MedGen: C0406727; Orphanet: 2753; OMIM: 258860

Name:: Joubert syndrome 18 (JBTS18)
Identifiers:: MONDO: MONDO:0013896; MedGen: C3553758; Orphanet: 2754; OMIM: 614815

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003783390	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 8, 2022)	germline	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

SCV003783390

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 8, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003783390.3

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

Description

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with TCTN3-related conditions. This variant is present in population databases (rs771545094, gnomAD 0.01%). This variant, c.1224_1226del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the TCTN3 protein (p.Gln408_Gly409delinsHis).

#	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: Mar 5, 2024

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