chr17-32997732-G-T
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_173847.5(SPACA3):c.602G>T(p.Cys201Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
SPACA3
NM_173847.5 missense
NM_173847.5 missense
Scores
6
7
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.06
Genes affected
SPACA3 (HGNC:16260): (sperm acrosome associated 3) The protein encoded by this gene is a sperm surface protein that may be involved in adhesion to the egg prior to fertilization. While the encoded protein has significant similarity to lysozyme at the amino acid level, it has no detectable bacteriocidal activity. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.98
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPACA3 | NM_173847.5 | c.602G>T | p.Cys201Phe | missense_variant | 5/5 | ENST00000269053.8 | |
SPACA3 | NM_001317225.2 | c.326G>T | p.Cys109Phe | missense_variant | 5/5 | ||
SPACA3 | NM_001317226.2 | c.293G>T | p.Cys98Phe | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPACA3 | ENST00000269053.8 | c.602G>T | p.Cys201Phe | missense_variant | 5/5 | 1 | NM_173847.5 | A2 | |
SPACA3 | ENST00000580599.5 | c.395G>T | p.Cys132Phe | missense_variant | 6/6 | 1 | P2 | ||
SPACA3 | ENST00000394637.2 | n.745G>T | non_coding_transcript_exon_variant | 5/5 | 1 | ||||
SPACA3 | ENST00000394638.1 | c.293G>T | p.Cys98Phe | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Sift4G
Pathogenic
D;D;D
Polyphen
1.0
.;D;.
Vest4
MutPred
0.88
.;Loss of ubiquitination at K204 (P = 0.0818);.;
MVP
MPC
0.47
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.