rs864622083

chr14-50628104-C-A

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Moderate

The NM_015915.5(ATL1):c.1193C>A(p.Ser398Tyr) 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S398F) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATL1 NM_015915.5 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1 U:1
• Conservation: PhyloP100: 6.08

Genes affected

ATL1 (HGNC:11231): (atlastin GTPase 1) The protein encoded by this gene is a GTPase and a Golgi body transmembrane protein. The encoded protein can form a homotetramer and has been shown to interact with spastin and with mitogen-activated protein kinase kinase kinase kinase 4. This protein may be involved in axonal maintenance as evidenced by the fact that defects in this gene are a cause of spastic paraplegia type 3. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_015915.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr14-50628104-C-T is described in Lovd as [Pathogenic].
• PP2: Missense variant where missense usually causes diseases, ATL1
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.957
• PP5: Variant 14-50628104-C-A is Pathogenic according to our data. Variant chr14-50628104-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 219428.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr14-50628104-C-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATL1	NM_015915.5	c.1193C>A	p.Ser398Tyr	missense_variant	12/14	ENST00000358385.12
ATL1	NM_001127713.1	c.1193C>A	p.Ser398Tyr	missense_variant	13/14
ATL1	NM_181598.4	c.1193C>A	p.Ser398Tyr	missense_variant	12/13
ATL1	XM_047431430.1	c.1193C>A	p.Ser398Tyr	missense_variant	13/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATL1	ENST00000358385.12	c.1193C>A	p.Ser398Tyr	missense_variant	12/14	1	NM_015915.5	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary spastic paraplegia 3A Pathogenic:1 Uncertain:1

Uncertain significance, no assertion criteria provided	literature only	Inherited Neuropathy Consortium Ii, University Of Miami	Jan 06, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jul 06, 2015	For these reasons, this variant has been classified as Likely Pathogenic. A different missense substitution at this codon (p.Ser398Phe) is reported to be deleterious (PMID: 19735987). This suggests that the serine residue is important for ATL1 protein function. This variant has been reported in the literature and is not present in population databases. This variant was reported in an individual affected with autosomal dominant hereditary spastic paraplegia, although it is unclear if this variant segregated with disease (PMID: 15596607). This sequence change replaces serine with tyrosine at codon 398 of the ATL1 protein (p.Ser398Tyr). The serine residue is moderately conserved and there is a large physicochemical difference between serine and tyrosine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.11
Cadd	Uncertain	25
Dann	Uncertain	1.0
Eigen	Pathogenic	0.72
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.95	D;D
M_CAP	Benign	0.018	T
MetaRNN	Pathogenic	0.96	D;D
MetaSVM	Benign	-0.56	T
MutationAssessor	Benign	1.3	L;L
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.70	T
PROVEAN	Uncertain	-3.3	D;D
REVEL	Uncertain	0.40
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Polyphen		0.99	.;D
Vest4		0.87
MutPred		0.83		Loss of disorder (P = 0.0122);Loss of disorder (P = 0.0122);
MVP		0.78
MPC		1.6
ClinPred		0.99	D
GERP RS		5.9
Varity_R		0.89
gMVP		0.89

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

Other links and lift over

dbSNP: rs864622083; hg19: chr14-51094822;