NM_012330.4(KAT6B):c.3730T>C (p.Cys1244Arg) AND Genitopatellar syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 20, 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:: RCV003646952.2

Allele description [Variation Report for NM_012330.4(KAT6B):c.3730T>C (p.Cys1244Arg)]

NM_012330.4(KAT6B):c.3730T>C (p.Cys1244Arg)

Gene:

KAT6B:lysine acetyltransferase 6B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.2

Genomic location:

Preferred name:

NM_012330.4(KAT6B):c.3730T>C (p.Cys1244Arg)

HGVS:

NC_000010.11:g.75028554T>C
NG_032048.1:g.207142T>C
NM_001256468.2:c.3181T>C
NM_001256469.2:c.2854T>C
NM_001370132.1:c.2692T>C
NM_001370133.1:c.2041T>C
NM_001370134.1:c.1645T>C
NM_001370135.1:c.1387T>C
NM_001370136.1:c.3730T>C
NM_001370137.1:c.3730T>C
NM_001370138.1:c.3181T>C
NM_001370139.1:c.2854T>C
NM_001370140.1:c.2854T>C
NM_001370141.1:c.2854T>C
NM_001370142.1:c.2854T>C
NM_001370143.1:c.2665T>C
NM_001370144.1:c.2665T>C
NM_012330.3:c.3730T>C
NM_012330.4:c.3730T>CMANE SELECT
NP_001243397.1:p.Cys1061Arg
NP_001243398.1:p.Cys952Arg
NP_001357061.1:p.Cys898Arg
NP_001357062.1:p.Cys681Arg
NP_001357063.1:p.Cys549Arg
NP_001357064.1:p.Cys463Arg
NP_001357065.1:p.Cys1244Arg
NP_001357066.1:p.Cys1244Arg
NP_001357067.1:p.Cys1061Arg
NP_001357068.1:p.Cys952Arg
NP_001357069.1:p.Cys952Arg
NP_001357070.1:p.Cys952Arg
NP_001357071.1:p.Cys952Arg
NP_001357072.1:p.Cys889Arg
NP_001357073.1:p.Cys889Arg
NP_036462.2:p.Cys1244Arg
NC_000010.10:g.76788312T>C

Protein change:

C1061R

Molecular consequence:

NM_001256468.2:c.3181T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001256469.2:c.2854T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370132.1:c.2692T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370133.1:c.2041T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370134.1:c.1645T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370135.1:c.1387T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370136.1:c.3730T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370137.1:c.3730T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370138.1:c.3181T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370139.1:c.2854T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370140.1:c.2854T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370141.1:c.2854T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370142.1:c.2854T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370143.1:c.2665T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370144.1:c.2665T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_012330.4:c.3730T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Genitopatellar syndrome (GTPTS)
Synonyms:: ABSENT PATELLAE, SCROTAL HYPOPLASIA, RENAL ANOMALIES, FACIAL DYSMORPHISM, AND MENTAL RETARDATION
Identifiers:: MONDO: MONDO:0011640; MedGen: C1853566; Orphanet: 85201; OMIM: 606170

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004519585	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 20, 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

SCV004519585

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 20, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004519585.1

#	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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt KAT6B protein function. This variant has not been reported in the literature in individuals affected with KAT6B-related conditions. This variant is present in population databases (rs751941544, gnomAD 0.0009%). This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 1244 of the KAT6B protein (p.Cys1244Arg).

#	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: Oct 8, 2024

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