NM_016169.4(SUFU):c.52_75del (p.10_17PGPTAPPA[1]) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 17, 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:: RCV001036934.8

Allele description [Variation Report for NM_016169.4(SUFU):c.52_75del (p.10_17PGPTAPPA[1])]

NM_016169.4(SUFU):c.52_75del (p.10_17PGPTAPPA[1])

Genes:

LOC130004614:ATAC-STARR-seq lymphoblastoid silent region 2764 [Gene]
SUFU:SUFU negative regulator of hedgehog signaling [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q24.32

Genomic location:

Preferred name:

NM_016169.4(SUFU):c.52_75del (p.10_17PGPTAPPA[1])

HGVS:

NC_000010.11:g.102504204_102504227del
NG_011901.1:g.3538_3561del
NG_021338.1:g.5243_5266del
NM_001178133.2:c.52_75del
NM_016169.4:c.52_75delMANE SELECT
NP_001171604.1:p.10_17PGPTAPPA[1]
NP_057253.2:p.10_17PGPTAPPA[1]
LRG_521t1:c.52_75del
LRG_521:g.5243_5266del
NC_000010.10:g.104263952_104263975del
NC_000010.10:g.104263961_104263984del
NM_016169.3:c.52_75del

Links:

dbSNP: rs1426839991

NCBI 1000 Genomes Browser:

rs1426839991

Molecular consequence:

NM_001178133.2:c.52_75del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_016169.4:c.52_75del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Gorlin syndrome
Synonyms:: Basal cell nevus syndrome
Identifiers:: MONDO: MONDO:0007187; MedGen: C0004779; Orphanet: 377; OMIM: PS109400

Name:: Medulloblastoma (MDB)
Synonyms:: Medulloblastoma, somatic; MEDULLOBLASTOMA PREDISPOSITION SYNDROME
Identifiers:: MONDO: MONDO:0007959; MeSH: D008527; MedGen: C0025149; Orphanet: 616; OMIM: 155255; Human Phenotype Ontology: HP:0002885

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001200323	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 17, 2023)	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

SCV001200323

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 17, 2023)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001200323.5

#	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. 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: 835932). This variant has not been reported in the literature in individuals affected with SUFU-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.52_75del, results in the deletion of 8 amino acid(s) of the SUFU protein (p.Pro18_Ala25del), but otherwise preserves the integrity of the reading frame.

#	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

ClinVar

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