NM_012330.4(KAT6B):c.4004C>T (p.Pro1335Leu) AND Genitopatellar syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 4, 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:: RCV003647074.2

Allele description [Variation Report for NM_012330.4(KAT6B):c.4004C>T (p.Pro1335Leu)]

NM_012330.4(KAT6B):c.4004C>T (p.Pro1335Leu)

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.4004C>T (p.Pro1335Leu)

HGVS:

NC_000010.11:g.75028828C>T
NG_032048.1:g.207416C>T
NM_001256468.2:c.3455C>T
NM_001256469.2:c.3128C>T
NM_001370132.1:c.2966C>T
NM_001370133.1:c.2315C>T
NM_001370134.1:c.1919C>T
NM_001370135.1:c.1661C>T
NM_001370136.1:c.4004C>T
NM_001370137.1:c.4004C>T
NM_001370138.1:c.3455C>T
NM_001370139.1:c.3128C>T
NM_001370140.1:c.3128C>T
NM_001370141.1:c.3128C>T
NM_001370142.1:c.3128C>T
NM_001370143.1:c.2939C>T
NM_001370144.1:c.2939C>T
NM_012330.4:c.4004C>TMANE SELECT
NP_001243397.1:p.Pro1152Leu
NP_001243398.1:p.Pro1043Leu
NP_001357061.1:p.Pro989Leu
NP_001357062.1:p.Pro772Leu
NP_001357063.1:p.Pro640Leu
NP_001357064.1:p.Pro554Leu
NP_001357065.1:p.Pro1335Leu
NP_001357066.1:p.Pro1335Leu
NP_001357067.1:p.Pro1152Leu
NP_001357068.1:p.Pro1043Leu
NP_001357069.1:p.Pro1043Leu
NP_001357070.1:p.Pro1043Leu
NP_001357071.1:p.Pro1043Leu
NP_001357072.1:p.Pro980Leu
NP_001357073.1:p.Pro980Leu
NP_036462.2:p.Pro1335Leu
NC_000010.10:g.76788586C>T

Protein change:

P1043L

Molecular consequence:

NM_001256468.2:c.3455C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001256469.2:c.3128C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370132.1:c.2966C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370133.1:c.2315C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370134.1:c.1919C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370135.1:c.1661C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370136.1:c.4004C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370137.1:c.4004C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370138.1:c.3455C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370139.1:c.3128C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370140.1:c.3128C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370141.1:c.3128C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370142.1:c.3128C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370143.1:c.2939C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370144.1:c.2939C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_012330.4:c.4004C>T - 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
SCV004537284	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 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

SCV004537284

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 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, SCV004537284.1

#	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 proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1335 of the KAT6B protein (p.Pro1335Leu). This variant is present in population databases (rs757599670, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with KAT6B-related conditions. 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. 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

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