NM_004260.4(RECQL4):c.554C>A (p.Ser185Tyr) AND Baller-Gerold syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 9, 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:: RCV003616199.2

Allele description [Variation Report for NM_004260.4(RECQL4):c.554C>A (p.Ser185Tyr)]

NM_004260.4(RECQL4):c.554C>A (p.Ser185Tyr)

Gene:

RECQL4:RecQ like helicase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_004260.4(RECQL4):c.554C>A (p.Ser185Tyr)

HGVS:

NC_000008.11:g.144516565G>T
NG_016430.2:g.6262C>A
NG_033083.1:g.3601G>T
NG_033083.2:g.3575G>T
NM_001413017.1:c.554C>A
NM_001413018.1:c.554C>A
NM_001413019.1:c.554C>A
NM_001413020.1:c.554C>A
NM_001413021.1:c.-366-152C>A
NM_001413022.1:c.-518C>A
NM_001413023.1:c.-518C>A
NM_001413024.1:c.-518C>A
NM_001413025.1:c.425C>A
NM_001413027.1:c.-580C>A
NM_001413028.1:c.-367+124C>A
NM_001413029.1:c.355-152C>A
NM_001413030.1:c.-580C>A
NM_001413031.1:c.-580C>A
NM_001413032.1:c.-580C>A
NM_001413033.1:c.554C>A
NM_001413034.1:c.-422C>A
NM_001413035.1:c.-518C>A
NM_001413036.1:c.554C>A
NM_001413037.1:c.-518C>A
NM_001413038.1:c.-518C>A
NM_001413039.1:c.554C>A
NM_001413040.1:c.-518C>A
NM_001413041.1:c.-580C>A
NM_001413042.1:c.-518C>A
NM_001413043.1:c.-787C>A
NM_004260.4:c.554C>AMANE SELECT
NP_001399946.1:p.Ser185Tyr
NP_001399947.1:p.Ser185Tyr
NP_001399948.1:p.Ser185Tyr
NP_001399949.1:p.Ser185Tyr
NP_001399954.1:p.Ser142Tyr
NP_001399962.1:p.Ser185Tyr
NP_001399965.1:p.Ser185Tyr
NP_001399968.1:p.Ser185Tyr
NP_004251.4:p.Ser185Tyr
LRG_277t1:c.554C>A
LRG_277:g.6262C>A
LRG_277p1:p.Ser185Tyr
NC_000008.10:g.145741949G>T
NR_182090.1:n.603C>A
NR_182091.1:n.603C>A
NR_182092.1:n.603C>A

Protein change:

S142Y

Molecular consequence:

NM_001413022.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413023.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413024.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413027.1:c.-580C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413030.1:c.-580C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413031.1:c.-580C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413032.1:c.-580C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413034.1:c.-422C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413035.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413037.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413038.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413040.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413041.1:c.-580C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413042.1:c.-518C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413043.1:c.-787C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001413021.1:c.-366-152C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001413028.1:c.-367+124C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001413029.1:c.355-152C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001413017.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413018.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413019.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413020.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413025.1:c.425C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413033.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413036.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001413039.1:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004260.4:c.554C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_182090.1:n.603C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182091.1:n.603C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182092.1:n.603C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Baller-Gerold syndrome (BGS)
Synonyms:: Craniosynostosis radial aplasia syndrome; Craniosynostosis with radial defects
Identifiers:: MONDO: MONDO:0009039; MedGen: C0265308; Orphanet: 1225; OMIM: 218600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004399392	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 9, 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

SCV004399392

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 9, 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, SCV004399392.1

#	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 expected to disrupt RECQL4 protein function. This variant has not been reported in the literature in individuals affected with RECQL4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 185 of the RECQL4 protein (p.Ser185Tyr).

#	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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