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NM_033343.4(LHX4):c.689G>A (p.Ser230Asn) AND Short stature-pituitary and cerebellar defects-small sella turcica syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 18, 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:
RCV004556022.1

Allele description [Variation Report for NM_033343.4(LHX4):c.689G>A (p.Ser230Asn)]

NM_033343.4(LHX4):c.689G>A (p.Ser230Asn)

Genes:
LHX4-AS1:LHX4 antisense RNA 1 [Gene - HGNC]
LHX4:LIM homeobox 4 [Gene - OMIM - HGNC]
ACBD6:acyl-CoA binding domain containing 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q25.2
Genomic location:
Preferred name:
NM_033343.4(LHX4):c.689G>A (p.Ser230Asn)
HGVS:
  • NC_000001.11:g.180271917G>A
  • NG_008081.1:g.46611G>A
  • NG_092783.1:g.504G>A
  • NM_033343.4:c.689G>AMANE SELECT
  • NP_203129.1:p.Ser230Asn
  • NP_203129.1:p.Ser230Asn
  • NC_000001.10:g.180241052G>A
  • NM_033343.3:c.689G>A
  • NR_037642.1:n.403C>T
Protein change:
S230N
Molecular consequence:
  • NM_033343.4:c.689G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037642.1:n.403C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Short stature-pituitary and cerebellar defects-small sella turcica syndrome (CPHD4)
Synonyms:
Pituitary hormone deficiency, combined 4; Pituitary hormone deficiency, combined with or without cerebellar defects; Short stature, pituitary and cerebellar defects and small sella turcica
Identifiers:
MONDO: MONDO:0009880; MedGen: C2678408; Orphanet: 85442; OMIM: 262700

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005045179Clinical Genomics Laboratory, Washington University in St. Louis
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 18, 2024) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV005045179.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The LHX4 c.689G>A (p.Ser230Asn) variant, to our knowledge, has not been reported in the medical literature. The highest population minor allele frequency in the population database genome aggregation database (v.2.1.1) is 0.003% in the European non-Finnish population. Computational predictors are uncertain as to the impact of this variant on LHX4 function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 26, 2024