NM_000168.6(GLI3):c.3115G>A (p.Ala1039Thr) AND multiple conditions

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (1 submission)
Last evaluated:: Sep 6, 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:: RCV000557052.6

Allele description

NM_000168.6(GLI3):c.3115G>A (p.Ala1039Thr)

Gene:

GLI3:GLI family zinc finger 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p14.1

Genomic location:

Preferred name:

NM_000168.6(GLI3):c.3115G>A (p.Ala1039Thr)

HGVS:

NC_000007.14:g.41965958C>T
NG_008434.1:g.276063G>A
NM_000168.6:c.3115G>AMANE SELECT
NP_000159.3:p.Ala1039Thr
NC_000007.13:g.42005556C>T
NM_000168.5:c.3115G>A

Protein change:

A1039T

Links:

dbSNP: rs770430876

NCBI 1000 Genomes Browser:

rs770430876

Molecular consequence:

NM_000168.6:c.3115G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Greig cephalopolysyndactyly syndrome (GCPS)
Synonyms:: Greig syndrome; Polysyndactyly with peculiar skull shape
Identifiers:: MONDO: MONDO:0008287; MedGen: C0265306; Orphanet: 380; OMIM: 175700

Name:: Pallister-Hall syndrome (PHS)
Synonyms:: Hypothalamic hamartoblastoma, hypopituitarism, imperforate anus, and postaxial polydactyly
Identifiers:: MONDO: MONDO:0007804; MedGen: C0265220; Orphanet: 672; OMIM: 146510

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000630796	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Sep 6, 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

SCV000630796

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Sep 6, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000630796.4

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

#	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: Feb 28, 2024

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