chrX-85107884-C-T

Position:

• chrX-85107884-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367857.2(SATL1):​c.1085G>A​(p.Arg362Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 24)
• Consequence: SATL1 NM_001367857.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.24

Genes affected

SATL1 (HGNC:27992): (spermidine/spermine N1-acetyl transferase like 1) Predicted to enable N-acetyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.047922313).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SATL1	NM_001367857.2	c.1085G>A	p.Arg362Lys	missense_variant	3/8	ENST00000644105.2
SATL1	NM_001367858.2	c.1085G>A	p.Arg362Lys	missense_variant	7/12
SATL1	NM_001012980.2	c.1085G>A	p.Arg362Lys	missense_variant	1/5
SATL1	XM_047442081.1	c.1085G>A	p.Arg362Lys	missense_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2	c.1085G>A	p.Arg362Lys	missense_variant	3/8		NM_001367857.2	A2

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 24

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 02, 2021

The c.1085G>A (p.R362K) alteration is located in exon 1 (coding exon 1) of the SATL1 gene. This alteration results from a G to A substitution at nucleotide position 1085, causing the arginine (R) at amino acid position 362 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.55	T
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.49
DEOGEN2	Benign	0.0023	T;.;.;.;.
FATHMM_MKL	Benign	0.042	N
LIST_S2	Benign	0.26	.;T;T;.;T
M_CAP	Benign	0.0014	T
MetaRNN	Benign	0.048	T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N;.;.;.;.
MutationTaster	Benign	1.0	N;N;N
PrimateAI	Benign	0.19	T
PROVEAN	Benign	0.15	N;N;.;.;.
REVEL	Benign	0.015
Sift	Benign	0.11	T;T;.;.;.
Sift4G	Benign	0.68	T;T;.;.;.
Polyphen		0.0	B;.;.;.;.
Vest4		0.026
MutPred		0.29		Gain of ubiquitination at R175 (P = 0.0051);.;.;.;.;
MVP		0.19
MPC		0.059
ClinPred		0.057	T
GERP RS		-2.0
Varity_R		0.071
gMVP		0.23

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-84362890;