NM_000368.5(TSC1):c.1309dup (p.His437fs) AND Tuberous sclerosis 1

Germline classification:: Likely pathogenic (1 submission)
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:: RCV002510744.2

Allele description [Variation Report for NM_000368.5(TSC1):c.1309dup (p.His437fs)]

NM_000368.5(TSC1):c.1309dup (p.His437fs)

Gene:

TSC1:TSC complex subunit 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_000368.5(TSC1):c.1309dup (p.His437fs)

HGVS:

NC_000009.12:g.132907326dup
NG_012386.1:g.42309dup
NM_000368.5:c.1309dupMANE SELECT
NM_001162426.2:c.1306dup
NM_001162427.2:c.1156dup
NM_001362177.2:c.946dup
NM_001406592.1:c.1308dup
NM_001406593.1:c.1308dup
NM_001406594.1:c.1308dup
NM_001406595.1:c.1308dup
NM_001406596.1:c.1308dup
NM_001406597.1:c.1305dup
NM_001406598.1:c.1305dup
NM_001406599.1:c.1305dup
NM_001406600.1:c.1305dup
NM_001406601.1:c.1308dup
NM_001406602.1:c.1308dup
NM_001406603.1:c.1305dup
NM_001406604.1:c.1305dup
NM_001406605.1:c.1308dup
NM_001406606.1:c.1308dup
NM_001406607.1:c.1308dup
NM_001406608.1:c.1305dup
NM_001406609.1:c.1305dup
NM_001406610.1:c.1155dup
NM_001406611.1:c.1152dup
NM_001406612.1:c.1152dup
NM_001406613.1:c.1152dup
NM_001406614.1:c.945dup
NM_001406615.1:c.945dup
NM_001406616.1:c.945dup
NM_001406617.1:c.945dup
NM_001406618.1:c.945dup
NM_001406619.1:c.945dup
NM_001406620.1:c.942dup
NM_001406621.1:c.942dup
NM_001406622.1:c.942dup
NM_001406623.1:c.942dup
NM_001406624.1:c.945dup
NM_001406625.1:c.942dup
NM_001406626.1:c.357dup
NM_001406627.1:c.354dup
NM_001406628.1:c.354dup
NM_001406629.1:c.255dup
NM_001406630.1:c.255dup
NP_000359.1:p.His437Profs
NP_000359.1:p.His437Profs
NP_000359.1:p.His437fs
NP_001155898.1:p.His436fs
NP_001155899.1:p.His386fs
NP_001349106.1:p.His316fs
NP_001393521.1:p.His437Profs
NP_001393522.1:p.His437Profs
NP_001393523.1:p.His437Profs
NP_001393524.1:p.His437Profs
NP_001393525.1:p.His437Profs
NP_001393526.1:p.His436Profs
NP_001393527.1:p.His436Profs
NP_001393528.1:p.His436Profs
NP_001393529.1:p.His436Profs
NP_001393530.1:p.His437Profs
NP_001393531.1:p.His437Profs
NP_001393532.1:p.His436Profs
NP_001393533.1:p.His436Profs
NP_001393534.1:p.His437Profs
NP_001393535.1:p.His437Profs
NP_001393536.1:p.His437Profs
NP_001393537.1:p.His436Profs
NP_001393538.1:p.His436Profs
NP_001393539.1:p.His386Profs
NP_001393540.1:p.His385Profs
NP_001393541.1:p.His385Profs
NP_001393542.1:p.His385Profs
NP_001393543.1:p.His316Profs
NP_001393544.1:p.His316Profs
NP_001393545.1:p.His316Profs
NP_001393546.1:p.His316Profs
NP_001393547.1:p.His316Profs
NP_001393548.1:p.His316Profs
NP_001393549.1:p.His315Profs
NP_001393550.1:p.His315Profs
NP_001393551.1:p.His315Profs
NP_001393552.1:p.His315Profs
NP_001393553.1:p.His316Profs
NP_001393554.1:p.His315Profs
NP_001393555.1:p.His120Profs
NP_001393556.1:p.His119Profs
NP_001393557.1:p.His119Profs
NP_001393558.1:p.His86Profs
NP_001393559.1:p.His86Profs
LRG_486t1:c.1308dup
LRG_486:g.42309dup
LRG_486p1:p.His437Profs
NC_000009.11:g.135782713dup
NM_000368.3:c.1308dup
NM_000368.4:c.1308dup
NM_000368.4:c.1309dupC
NR_176214.1:n.1525dup
NR_176215.1:n.1525dup
NR_176216.1:n.1392dup
NR_176217.1:n.1522dup
NR_176218.1:n.1525dup

Protein change:

H316fs

Molecular consequence:

NM_000368.5:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001162426.2:c.1306dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001162427.2:c.1156dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001362177.2:c.946dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406592.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406593.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406594.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406595.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406596.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406597.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406598.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406599.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406600.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406601.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406602.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406603.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406604.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406605.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406606.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406607.1:c.1308dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406608.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406609.1:c.1305dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406610.1:c.1155dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406611.1:c.1152dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406612.1:c.1152dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406613.1:c.1152dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406614.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406615.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406616.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406617.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406618.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406619.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406620.1:c.942dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406621.1:c.942dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406622.1:c.942dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406623.1:c.942dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406624.1:c.945dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406625.1:c.942dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406626.1:c.357dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406627.1:c.354dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406628.1:c.354dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406629.1:c.255dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406630.1:c.255dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Tuberous sclerosis 1 (TSC1)
Identifiers:: MONDO: MONDO:0008612; MedGen: C1854465; Orphanet: 805; OMIM: 191100

Recent activity

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Polygalacturonase [Bacteroides thetaiotaomicron]
Polygalacturonase [Bacteroides thetaiotaomicron]
gi|938477943|gnl|Prokka|Btheta7330_ |gb|ALJ42175.1|

Protein
unknown [Glycine max]
unknown [Glycine max]
gi|255635243|gb|ACU17976.1|

Protein
Os03g0833800 [Oryza sativa Japonica Group]
Os03g0833800 [Oryza sativa Japonica Group]
gi|937912312|dbj|BAS87232.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002820303	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	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

SCV002820303

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

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	yes	not provided	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 Neuberg Centre For Genomic Medicine, NCGM, SCV002820303.1

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

Description

The frameshift duplication p.H437Pfs*5 in TSC1 (NM_000368.5) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.H437Pfs*5 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation. For these reasons, this variant has been classified as Likely Pathogenic.

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

Last Updated: Apr 6, 2024

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Relating variation to medicine