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NM_020800.3(IFT80):c.1093A>G (p.Thr365Ala) AND Asphyxiating thoracic dystrophy 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 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:
RCV001803759.8

Allele description [Variation Report for NM_020800.3(IFT80):c.1093A>G (p.Thr365Ala)]

NM_020800.3(IFT80):c.1093A>G (p.Thr365Ala)

Genes:
TRIM59-IFT80:TRIM59-IFT80 readthrough (NMD candidate) [Gene - HGNC]
IFT80:intraflagellar transport 80 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q25.33
Genomic location:
Preferred name:
NM_020800.3(IFT80):c.1093A>G (p.Thr365Ala)
HGVS:
  • NC_000003.12:g.160303973T>C
  • NG_022932.1:g.100560A>G
  • NM_001190241.2:c.682A>G
  • NM_001190242.2:c.682A>G
  • NM_020800.3:c.1093A>GMANE SELECT
  • NP_001177170.1:p.Thr228Ala
  • NP_001177171.1:p.Thr228Ala
  • NP_065851.1:p.Thr365Ala
  • NC_000003.11:g.160021761T>C
  • NM_020800.2:c.1093A>G
  • NR_148401.1:n.1801A>G
  • NR_148402.1:n.3337A>G
  • NR_148403.1:n.3604A>G
Protein change:
T228A
Links:
dbSNP: rs140202230
NCBI 1000 Genomes Browser:
rs140202230
Molecular consequence:
  • NM_001190241.2:c.682A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001190242.2:c.682A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020800.3:c.1093A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148401.1:n.1801A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148402.1:n.3337A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148403.1:n.3604A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Asphyxiating thoracic dystrophy 2 (SRTD2)
Synonyms:
SHORT-RIB THORACIC DYSPLASIA 2 WITH OR WITHOUT POLYDACTYLY; SHORT-RIB THORACIC DYSPLASIA 2 WITH POLYDACTYLY; SHORT-RIB THORACIC DYSPLASIA 2 WITHOUT POLYDACTYLY
Identifiers:
MONDO: MONDO:0012644; MedGen: C1970005; Orphanet: 474; OMIM: 611263

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002048912ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)		Uncertain significance
(May 4, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048912.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The IFT80 c.1093A>G; p.Thr365Ala variant (rs140202230) was reported as compound heterozygous with another disease-associated variant in two individuals affected with short-rib polydactyly syndrome type IV or asphyxiating thoracic dystrophy (Zhang 2018). However, phasing was not confirmed in these reports. This variant is also reported in ClinVar (Variation ID: 406217) and is found in the general population with an overall allele frequency of 0.008% (23/282,476 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.492). However, given the lack of clinical and functional data, the significance of the p.Thr365Ala variant is uncertain at this time. References: Zhang et al. Expanding the genetic architecture and phenotypic spectrum in the skeletal ciliopathies. Hum Mutat. 2018 Jan;39(1):152-166. PMID: 29068549.

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

Last Updated: Oct 13, 2024