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NM_000548.5(TSC2):c.4590G>T (p.Ser1530=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 22, 2021
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:
RCV004476379.1

Allele description [Variation Report for NM_000548.5(TSC2):c.4590G>T (p.Ser1530=)]

NM_000548.5(TSC2):c.4590G>T (p.Ser1530=)

Gene:
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.4590G>T (p.Ser1530=)
HGVS:
  • NC_000016.10:g.2085250G>T
  • NG_005895.1:g.40945G>T
  • NM_000548.5:c.4590G>TMANE SELECT
  • NM_001077183.3:c.4389G>T
  • NM_001114382.3:c.4521G>T
  • NM_001318827.2:c.4281G>T
  • NM_001318829.2:c.4245G>T
  • NM_001318831.2:c.3858G>T
  • NM_001318832.2:c.4422G>T
  • NM_001363528.2:c.4392G>T
  • NM_001370404.1:c.4458G>T
  • NM_001370405.1:c.4461G>T
  • NM_001406663.1:c.4587G>T
  • NM_001406664.1:c.4518G>T
  • NM_001406665.1:c.4512G>T
  • NM_001406667.1:c.4482G>T
  • NM_001406668.1:c.4479G>T
  • NM_001406670.1:c.4410G>T
  • NM_001406671.1:c.4380G>T
  • NM_001406673.1:c.4377G>T
  • NM_001406675.1:c.4374G>T
  • NM_001406676.1:c.4371G>T
  • NM_001406677.1:c.4332G>T
  • NM_001406678.1:c.4278G>T
  • NM_001406679.1:c.4242G>T
  • NM_001406680.1:c.3990G>T
  • NM_001406681.1:c.3930G>T
  • NM_001406682.1:c.3921G>T
  • NM_001406683.1:c.3921G>T
  • NM_001406684.1:c.3918G>T
  • NM_001406685.1:c.3792G>T
  • NM_001406686.1:c.3792G>T
  • NM_001406687.1:c.3789G>T
  • NM_001406688.1:c.3789G>T
  • NM_001406689.1:c.3177G>T
  • NM_001406690.1:c.3117G>T
  • NM_001406691.1:c.3114G>T
  • NM_001406692.1:c.3048G>T
  • NM_001406693.1:c.3048G>T
  • NM_001406694.1:c.3048G>T
  • NM_001406695.1:c.3045G>T
  • NM_001406696.1:c.3045G>T
  • NM_001406697.1:c.3045G>T
  • NM_001406698.1:c.2787G>T
  • NM_021055.3:c.4461G>T
  • NP_000539.2:p.Ser1530=
  • NP_000539.2:p.Ser1530=
  • NP_001070651.1:p.Ser1463=
  • NP_001107854.1:p.Ser1507=
  • NP_001305756.1:p.Ser1427=
  • NP_001305758.1:p.Ser1415=
  • NP_001305760.1:p.Ser1286=
  • NP_001305761.1:p.Ser1474=
  • NP_001350457.1:p.Ser1464=
  • NP_001357333.1:p.Ser1486=
  • NP_001357334.1:p.Ser1487=
  • NP_001393592.1:p.Ser1529=
  • NP_001393593.1:p.Ser1506=
  • NP_001393594.1:p.Ser1504=
  • NP_001393596.1:p.Ser1494=
  • NP_001393597.1:p.Ser1493=
  • NP_001393599.1:p.Ser1470=
  • NP_001393600.1:p.Ser1460=
  • NP_001393602.1:p.Ser1459=
  • NP_001393604.1:p.Ser1458=
  • NP_001393605.1:p.Ser1457=
  • NP_001393606.1:p.Ser1444=
  • NP_001393607.1:p.Ser1426=
  • NP_001393608.1:p.Ser1414=
  • NP_001393609.1:p.Ser1330=
  • NP_001393610.1:p.Ser1310=
  • NP_001393611.1:p.Ser1307=
  • NP_001393612.1:p.Ser1307=
  • NP_001393613.1:p.Ser1306=
  • NP_001393614.1:p.Ser1264=
  • NP_001393615.1:p.Ser1264=
  • NP_001393616.1:p.Ser1263=
  • NP_001393617.1:p.Ser1263=
  • NP_001393618.1:p.Ser1059=
  • NP_001393619.1:p.Ser1039=
  • NP_001393620.1:p.Ser1038=
  • NP_001393621.1:p.Ser1016=
  • NP_001393622.1:p.Ser1016=
  • NP_001393623.1:p.Ser1016=
  • NP_001393624.1:p.Ser1015=
  • NP_001393625.1:p.Ser1015=
  • NP_001393626.1:p.Ser1015=
  • NP_001393627.1:p.Ser929=
  • NP_066399.2:p.Ser1487=
  • LRG_487t1:c.4590G>T
  • LRG_487:g.40945G>T
  • LRG_487p1:p.Ser1530=
  • NC_000016.9:g.2135251G>T
  • NM_000548.3:c.4590G>T
  • NR_176225.1:n.4542G>T
  • NR_176226.1:n.4790G>T
  • NR_176227.1:n.4718G>T
  • NR_176228.1:n.4539G>T
  • NR_176229.1:n.4499G>T
Molecular consequence:
  • NR_176225.1:n.4542G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176226.1:n.4790G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176227.1:n.4718G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176228.1:n.4539G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176229.1:n.4499G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000548.5:c.4590G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001077183.3:c.4389G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001114382.3:c.4521G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318827.2:c.4281G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318829.2:c.4245G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318831.2:c.3858G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318832.2:c.4422G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363528.2:c.4392G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370404.1:c.4458G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370405.1:c.4461G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406663.1:c.4587G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406664.1:c.4518G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406665.1:c.4512G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406667.1:c.4482G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406668.1:c.4479G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406670.1:c.4410G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406671.1:c.4380G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406673.1:c.4377G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406675.1:c.4374G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406676.1:c.4371G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406677.1:c.4332G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406678.1:c.4278G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406679.1:c.4242G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406680.1:c.3990G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406681.1:c.3930G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406682.1:c.3921G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406683.1:c.3921G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406684.1:c.3918G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406685.1:c.3792G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406686.1:c.3792G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406687.1:c.3789G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406688.1:c.3789G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406689.1:c.3177G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406690.1:c.3117G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406691.1:c.3114G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406692.1:c.3048G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406693.1:c.3048G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406694.1:c.3048G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406695.1:c.3045G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406696.1:c.3045G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406697.1:c.3045G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406698.1:c.2787G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_021055.3:c.4461G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004971746Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 22, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV004971746.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.4590G>T (p.S1530S) alteration is located in exon 36 (coding exon 35) of the TSC2 gene. This alteration consists of a G to T substitution at nucleotide position 4590. This nucleotide substitution does not change the amino acid at codon 1530. However, this change occurs in the last nucleotide of Exon 36 (c.4570_4662) which makes it likely to have some effect on normal mRNA splicing. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024