chr12-51705532-A-C

Variant names:

• chr12-51705532-A-C
• rs878854973
• NM_001330260.2:c.1250A>C
• SCN8A p.Gln417Pro

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+5 Uncertain · Hot

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 5 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateO6_SupportingO7_SupportingO8_Supporting

The NM_001330260.2(SCN8A):c.1250A>C (p.Gln417Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The gene SCN8A is a cancer driver gene (CancerMine: 1 driver citations). 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. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 9.32). Variant has been reported in ClinVar as Pathogenic/Likely Pathogenic (no review stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCN8A NM_001330260.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: 9.32
• Publications: 3 publications found

Genes affected

SCN8A (HGNC:10596): (sodium voltage-gated channel alpha subunit 8) This gene encodes a member of the sodium channel alpha subunit gene family. The encoded protein forms the ion pore region of the voltage-gated sodium channel. This protein is essential for the rapid membrane depolarization that occurs during the formation of the action potential in excitable neurons. Mutations in this gene are associated with cognitive disability, pancerebellar atrophy and ataxia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

SCN8A Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, ClinGen
• developmental and epileptic encephalopathy, 13

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Ambry Genetics, PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
• cognitive impairment with or without cerebellar ataxia

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• seizures, benign familial infantile, 5

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• benign familial infantile epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• undetermined early-onset epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• myoclonus, familial, 2

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

Classification according to ACGS-UK Somatic Oncogenicity v2025

Specifications for SCN8A are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 5 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
	O6Computational evidence supports deleterious effect		Computational evidence supports a deleterious/oncogenic effect; Missense variant — primary computational scorer supports an oncogenic/deleterious effect
	O7Mutational hotspot or critical domain		Supporting: cancerhotspots.org hit, critical domain, or missense neighbourhood hotspot; No cancerhotspots.org hit at this position; UniProt domain: 0 pathogenic, 0 benign.; ±8 AA neighbourhood: 8 pathogenic, 0 benign (OR vs. background: 85.0); Variant does not impact splicing — splice-hotspot path not applicable
	O8Missense constraint in gene or region		Missense in gene/domain constrained for missense variation where missense is common disease mechanism (O8 supporting); Gene/disease mechanism: missense is a common mechanism of oncogenesis; gnomAD missense Z-score: 10.45 (threshold ≥3.09 for constraint); Domain-level constraint: variant is in a critically constrained functional domain (IS_AT_CRITICAL_DOMAIN)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_001330260.2. 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
	SCN8A NM_001330260.2	MANE Select	c.1250A>C p.Gln417Pro	missense	Exon 10 of 27	Prot: NP_001317189.1 UniProt:
	SCN8A NM_014191.4	MANE Plus Clinical	c.1250A>C p.Gln417Pro	missense	Exon 10 of 27	Prot: NP_055006.1 UniProt:
	SCN8A NM_001177984.3		c.1250A>C p.Gln417Pro	missense	Exon 10 of 26	Prot: NP_001171455.1 UniProt:

SCN8A NM_001330260.2

MANE Select

HGVSc / HGVSpc.1250A>Cp.Gln417Pro

Exon rankExon 10 of 27

missense

Prot: NP_001317189.1UniProt: Q9UQD0-2

SCN8A NM_014191.4

MANE Plus Clinical

HGVSc / HGVSpc.1250A>Cp.Gln417Pro

Exon rankExon 10 of 27

missense

Prot: NP_055006.1UniProt: Q9UQD0-1

SCN8A NM_001177984.3

HGVSc / HGVSpc.1250A>Cp.Gln417Pro

Exon rankExon 10 of 26

missense

Prot: NP_001171455.1UniProt: Q9UQD0-5

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	SCN8A ENST00000354534.11	TSL:1MANE Plus Clinical	c.1250A>C p.Gln417Pro	missense	Exon 10 of 27	Prot: ENSP00000346534.4 UniProt:
	SCN8A ENST00000627620.5	TSL:5MANE Select	c.1250A>C p.Gln417Pro	missense	Exon 10 of 27	Prot: ENSP00000487583.2 UniProt:
	SCN8A ENST00000599343.5	TSL:5	c.1250A>C p.Gln417Pro	missense	Exon 9 of 26	Prot: ENSP00000476447.3 UniProt:

SCN8A ENST00000354534.11

TSL:1MANE Plus Clinical

HGVSc / HGVSpc.1250A>Cp.Gln417Pro

Exon rankExon 10 of 27

missense

Prot: ENSP00000346534.4UniProt: Q9UQD0-1

SCN8A ENST00000627620.5

TSL:5MANE Select

HGVSc / HGVSpc.1250A>Cp.Gln417Pro

Exon rankExon 10 of 27

missense

Prot: ENSP00000487583.2UniProt: Q9UQD0-2

SCN8A ENST00000599343.5

TSL:5

HGVSc / HGVSpc.1250A>Cp.Gln417Pro

Exon rankExon 9 of 26

missense

Prot: ENSP00000476447.3UniProt: Q9UQD0-3

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:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
1	-	-	Early-infantile DEE (1)
-	1	-	Inborn genetic diseases (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	28
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D
Eigen	Pathogenic	0.84
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Uncertain	0.96	D
FuncVEP CTI	Pathogenic	1.0
GPN-Star LLR	N/A	-11
GPN-Star score	N/A	11
LIST_S2	Uncertain	0.97	D
M_CAP	Pathogenic	0.81	D
MetaRNN	Pathogenic	0.88	D
MetaSVM	Pathogenic	1.1	D
Mutation Taster	N/A	3/97	disease causing (ClinVar)
MutationAssessor	Pathogenic	3.1	M
PhyloP100	Pathogenic	9.3
popEVE	Pathogenic	-6.0
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-5.9	D
REVEL	Pathogenic	0.90
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0030	D
Varity_R	N/A	0.98
VESM-3B	Benign	-17

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 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: rs878854973;

hg19: chr12-52099316;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar