rs886037653

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The ENST00000388798.7(SPAG1):​c.2542del​(p.Asp848IlefsTer10) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

SPAG1
ENST00000388798.7 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 6.83
Variant links:
Genes affected
SPAG1 (HGNC:11212): (sperm associated antigen 1) The correlation of anti-sperm antibodies with cases of unexplained infertility implicates a role for these antibodies in blocking fertilization. Improved diagnosis and treatment of immunologic infertility, as well as identification of proteins for targeted contraception, are dependent on the identification and characterization of relevant sperm antigens. The protein expressed by this gene is recognized by anti-sperm agglutinating antibodies from an infertile woman. Furthermore, immunization of female rats with the recombinant human protein reduced fertility. This protein localizes to the plasma membrane of germ cells in the testis and to the post-acrosomal plasma membrane of mature spermatozoa. Recombinant polypeptide binds GTP and exhibits GTPase activity. Thus, this protein may regulate GTP signal transduction pathways involved in spermatogenesis and fertilization. Two transcript variants of this gene encode the same protein. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 8-100240660-AG-A is Pathogenic according to our data. Variant chr8-100240660-AG-A is described in ClinVar as [Pathogenic]. Clinvar id is 88684.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPAG1NM_003114.5 linkuse as main transcriptc.2542del p.Asp848IlefsTer10 frameshift_variant 18/19 ENST00000388798.7 NP_003105.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPAG1ENST00000388798.7 linkuse as main transcriptc.2542del p.Asp848IlefsTer10 frameshift_variant 18/191 NM_003114.5 ENSP00000373450 P1Q07617-1
SPAG1ENST00000251809.4 linkuse as main transcriptc.2542del p.Asp848IlefsTer10 frameshift_variant 18/195 ENSP00000251809 P1Q07617-1
SPAG1ENST00000519409.1 linkuse as main transcriptn.106del non_coding_transcript_exon_variant 1/23

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
36
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Primary ciliary dyskinesia 28 Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 22, 2019For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SPAG1 are known to be pathogenic (PMID: 24055112). This variant has been observed in individual(s) with primary ciliary dyskinesia (PMID: 24055112). ClinVar contains an entry for this variant (Variation ID: 88684). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Asp848Ilefs*10) in the SPAG1 gene. It is expected to result in an absent or disrupted protein product. -
Autosomal dominant nocturnal frontal lobe epilepsy 5 Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMOct 03, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs886037653; hg19: chr8-101252888; API