NM_016169.4(SUFU):c.38C>G (p.Thr13Ser) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 3, 2024
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:: RCV002048729.6

Allele description [Variation Report for NM_016169.4(SUFU):c.38C>G (p.Thr13Ser)]

NM_016169.4(SUFU):c.38C>G (p.Thr13Ser)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.32

Genomic location:

Preferred name:

NM_016169.4(SUFU):c.38C>G (p.Thr13Ser)

HGVS:

NC_000010.11:g.102504190C>G
NG_011901.1:g.3566G>C
NG_021338.1:g.5229C>G
NM_001178133.2:c.38C>G
NM_016169.4:c.38C>GMANE SELECT
NP_001171604.1:p.Thr13Ser
NP_057253.2:p.Thr13Ser
LRG_521t1:c.38C>G
LRG_521:g.5229C>G
NC_000010.10:g.104263947C>G
NM_016169.3:c.38C>G

Protein change:

T13S

Links:

dbSNP: rs768935165

NCBI 1000 Genomes Browser:

rs768935165

Molecular consequence:

NM_001178133.2:c.38C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_016169.4:c.38C>G - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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Rattus norvegicus FERM domain containing 8 (Frmd8), mRNA
Rattus norvegicus FERM domain containing 8 (Frmd8), mRNA
gi|56605771|ref|NM_001008348.1|

Nucleotide
Sesbania sp. Bidgood 2711 small subunit ribosomal RNA gene, partial sequence; in...
Sesbania sp. Bidgood 2711 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|499061881|gb|JX453707.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002310950	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 3, 2024)	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

SCV002310950

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 3, 2024)

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, SCV002310950.3

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

Description

This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 13 of the SUFU protein (p.Thr13Ser). This variant is present in population databases (rs768935165, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with SUFU-related conditions. ClinVar contains an entry for this variant (Variation ID: 1522672). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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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