chr19-41970540-G-T

Variant names:

• chr19-41970540-G-T
• rs1064797245
• NM_152296.5:c.2266C>A
• ATP1A3 p.Arg756Ser

GermlineCancer (beta)

Variant summary

Our verdict is Pathogenic.

+10 Pathogenic

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 10 classification points (ACMG Germline Pathogenicity v2019). PM1PM2PM5PP2PP3PP5_Moderate

The NM_152296.5(ATP1A3):c.2266C>A (p.Arg756Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely damaging/oncogenic. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 8.03). Variant has been reported in ClinVar as Pathogenic/Likely Pathogenic (★). A different missense at the same amino acid position has been reported as Pathogenic/Likely Pathogenic in ClinVar: p.R756H: Pathogenic/Likely_pathogenic (ClinVar VariationId 161134, 2 stars)

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATP1A3 NM_152296.5 missense, splice_region
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.03
• Publications: 1 publications found

Genes affected

ATP1A3 (HGNC:801): (ATPase Na+/K+ transporting subunit alpha 3) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 3 subunit. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ATP1A3 Gene-Disease associations (from GenCC):

• alternating hemiplegia of childhood 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Ambry Genetics
• ATP1A3-associated neurological disorder

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, ClinGen, Illumina
• cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics, Orphanet
• developmental and epileptic encephalopathy 99

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• dystonia 12

  Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics, Orphanet
• encephalopathy, acute, infection-induced

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• alternating hemiplegia of childhood

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• complex neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000285505 (HGNC:):

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Pathogenic. The variant received 10 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM1Mutational hot spot or critical domain		Missense neighbourhood hotspot (≥2 P/LP within ±8 AA, OR ≥ 5 vs. background) — PM1; In-domain: 0 pathogenic, 0 benign rare missense variants.; ±8 AA neighbourhood: 6 pathogenic, 0 benign (OR vs. background: 65.0).
	PM2Absent/extremely low in population databases		Absent from gnomAD (AD/XL gene) — PM2; Absent from gnomAD at well-covered site (MOI: AD+AR) (threshold 0.0001) — PM2 moderate.
	PM5Novel missense at known pathogenic residue		Different pathogenic missense at same AA residue in ClinVar (PM5); ClinVar contains a germline Pathogenic/Likely Pathogenic entry at the same amino acid position with a different amino acid change: p.R756H: Pathogenic/Likely_pathogenic (ClinVar VariationId 161134, 2 stars)
	PP2Missense in gene with low missense rate		Missense in gene constrained for missense variation where missense is common disease mechanism (PP2); Missense in a gene constrained for missense variation (gnomAD Z-score: 9.135). ClinVar shows strong pathogenic missense enrichment: 152 P/LP and 24 B/LB missense entries (ratio 6.3×).
	PP3Computational evidence supports damaging effect		Splicing predictors (SpliceAI/dbscSNV) support splicing impact — supporting computational evidence (PP3); Splicing verdict: pathogenic (Supporting).; Germline computational verdict: pathogenic (Strong).
	PP5Reputable source reports pathogenic		ClinVar 1-star pathogenic — moderate (PP5); ClinVar germline classification: Pathogenic/Likely Pathogenic, 1 star(s).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_152296.5. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ATP1A3 NM_152296.5	MANE Select	c.2266C>A p.Arg756Ser	missensesplice_region	Exon 17 of 23	Prot: NP_689509.1 UniProt:
	ATP1A3 NM_001256214.2		c.2305C>A p.Arg769Ser	missensesplice_region	Exon 17 of 23	Prot: NP_001243143.1 UniProt:
	ATP1A3 NM_001256213.2		c.2299C>A p.Arg767Ser	missensesplice_region	Exon 17 of 23	Prot: NP_001243142.1 UniProt:

ATP1A3 NM_152296.5

MANE Select

HGVSc / HGVSpc.2266C>Ap.Arg756Ser

Exon rankExon 17 of 23

missensesplice_region

Prot: NP_689509.1UniProt: P13637-1

ATP1A3 NM_001256214.2

HGVSc / HGVSpc.2305C>Ap.Arg769Ser

Exon rankExon 17 of 23

missensesplice_region

Prot: NP_001243143.1UniProt: P13637-3

ATP1A3 NM_001256213.2

HGVSc / HGVSpc.2299C>Ap.Arg767Ser

Exon rankExon 17 of 23

missensesplice_region

Prot: NP_001243142.1UniProt: P13637-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	ATP1A3 ENST00000648268.1	MANE Select	c.2266C>A p.Arg756Ser	missensesplice_region	Exon 17 of 23	Prot: ENSP00000498113.1 UniProt:
	ENSG00000285505 ENST00000644613.1		n.2266C>A	splice_regionnon_coding_transcript_exon	Exon 17 of 25	Prot: ENSP00000494711.1 UniProt:
	ATP1A3 ENST00000545399.6	TSL:2	c.2305C>A p.Arg769Ser	missensesplice_region	Exon 17 of 23	Prot: ENSP00000444688.1 UniProt:

ATP1A3 ENST00000648268.1

MANE Select

HGVSc / HGVSpc.2266C>Ap.Arg756Ser

Exon rankExon 17 of 23

missensesplice_region

Prot: ENSP00000498113.1UniProt: P13637-1

ENSG00000285505 ENST00000644613.1

HGVSc / HGVSpn.2266C>A

Exon rankExon 17 of 25

splice_regionnon_coding_transcript_exon

Prot: ENSP00000494711.1UniProt: A0A2R8YEY8

ATP1A3 ENST00000545399.6

TSL:2

HGVSc / HGVSpc.2305C>Ap.Arg769Ser

Exon rankExon 17 of 23

missensesplice_region

Prot: ENSP00000444688.1UniProt: P13637-3

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:34
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

ClinVar submissions

Significance: Likely pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Alternating hemiplegia of childhood 2 (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	34
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
CADD	Pathogenic	35
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.83	D
Eigen	Pathogenic	0.95
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.98	D
FuncVEP CTI	Pathogenic	0.98
GPN-Star LLR	N/A	-9.8
GPN-Star score	N/A	9.8
LIST_S2	Benign	0.85	D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.0	D
Mutation Taster	N/A	2/98	disease causing
MutationAssessor	Pathogenic	5.0	H
PhyloP100	Pathogenic	8.0
popEVE	Pathogenic	-5.8
PrimateAI	Pathogenic	0.89	D
PROVEAN	Pathogenic	-4.5	D
REVEL	Pathogenic	0.96
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Varity_R	N/A	0.88
VESM-3B	Benign	-14

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
DS_AG_spliceai	Pathogenic	0.77	Position offset: -2
Pangolin (max)	Uncertain	0.39
Pangolin gain	Uncertain	0.39	Position offset: -2
SpliceAI score (max)	Pathogenic	0.77	Details are displayed if max score is > 0.2

Showing 4 of 4 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs1064797245;

hg19: chr19-42474692;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar