NM_003114.5(SPAG1):c.1406C>G (p.Ser469Trp) AND Primary ciliary dyskinesia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 14, 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:: RCV002395681.3

Allele description [Variation Report for NM_003114.5(SPAG1):c.1406C>G (p.Ser469Trp)]

NM_003114.5(SPAG1):c.1406C>G (p.Ser469Trp)

Genes:

LOC130000832:ATAC-STARR-seq lymphoblastoid silent region 19412 [Gene]
SPAG1:sperm associated antigen 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q22.2

Genomic location:

Preferred name:

NM_003114.5(SPAG1):c.1406C>G (p.Ser469Trp)

HGVS:

NC_000008.11:g.100213399C>G
NG_033834.2:g.60365C>G
NM_001374321.1:c.1406C>G
NM_003114.5:c.1406C>GMANE SELECT
NM_172218.3:c.1406C>G
NP_001361250.1:p.Ser469Trp
NP_003105.2:p.Ser469Trp
NP_757367.1:p.Ser469Trp
NC_000008.10:g.101225627C>G
NG_033834.1:g.60365C>G
NM_172218.2:c.1406C>G

Protein change:

S469W

Links:

dbSNP: rs756472753

NCBI 1000 Genomes Browser:

rs756472753

Molecular consequence:

NM_001374321.1:c.1406C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003114.5:c.1406C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_172218.3:c.1406C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Primary ciliary dyskinesia
Synonyms:: Ciliary dyskinesia
Identifiers:: MONDO: MONDO:0016575; MedGen: C0008780; OMIM: PS244400; Human Phenotype Ontology: HP:0012265

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002698904	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 14, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002698904

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 14, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002698904.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The p.S469W variant (also known as c.1406C>G), located in coding exon 10 of the SPAG1 gene, results from a C to G substitution at nucleotide position 1406. The serine at codon 469 is replaced by tryptophan, an amino acid with highly dissimilar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 12, 2024

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