1-46672945-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001145474.4(TEX38):āc.110A>Gā(p.His37Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,150 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Consequence
TEX38
NM_001145474.4 missense
NM_001145474.4 missense
Scores
3
8
4
Clinical Significance
Conservation
PhyloP100: 4.87
Genes affected
TEX38 (HGNC:29589): (testis expressed 38) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
ATPAF1 (HGNC:18803): (ATP synthase mitochondrial F1 complex assembly factor 1) This gene encodes an assembly factor for the F(1) component of the mitochondrial ATP synthase. This protein binds specifically to the F1 beta subunit and is thought to prevent this subunit from forming nonproductive homooligomers during enzyme assembly. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX38 | NM_001145474.4 | c.110A>G | p.His37Arg | missense_variant | 2/2 | ENST00000334122.5 | NP_001138946.1 | |
TEX38 | XM_011541421.4 | c.113A>G | p.His38Arg | missense_variant | 2/2 | XP_011539723.1 | ||
TEX38 | NM_001300863.2 | c.-46-7A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001287792.1 | ||||
TEX38 | NM_001300864.2 | c.-40-79A>G | intron_variant | NP_001287793.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX38 | ENST00000334122.5 | c.110A>G | p.His37Arg | missense_variant | 2/2 | 1 | NM_001145474.4 | ENSP00000455854 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 31
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.110A>G (p.H37R) alteration is located in exon 2 (coding exon 2) of the TEX38 gene. This alteration results from a A to G substitution at nucleotide position 110, causing the histidine (H) at amino acid position 37 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MutationAssessor
Benign
.;L
MutationTaster
Benign
D;D;D;N;N
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
0.99
.;D
Vest4
0.62
MVP
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at