chr9-92047261-G-A

Variant names:

• chr9-92047261-G-A
• rs267607087
• NM_006415.4:c.992C>T

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Moderate

The NM_006415.4(SPTLC1):​c.992C>T​(p.Ser331Phe) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S331Y) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SPTLC1 NM_006415.4 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:3
• Conservation: PhyloP100: 9.66
• Publications: 37 publications found

Genes affected

SPTLC1 (HGNC:11277): (serine palmitoyltransferase long chain base subunit 1) This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]

SPTLC1 Gene-Disease associations (from GenCC):

• amyotrophic lateral sclerosis 27, juvenile

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• neuropathy, hereditary sensory and autonomic, type 1A

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• hereditary sensory and autonomic neuropathy type 1

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_006415.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr9-92047261-G-T is described in CliVar as Pathogenic. Clinvar id is 372788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.918
• PP5: Variant 9-92047261-G-A is Pathogenic according to our data. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92047261-G-A is described in CliVar as Pathogenic. Clinvar id is 4804.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTLC1	NM_006415.4	c.992C>T	p.Ser331Phe	missense_variant	Exon 11 of 15	ENST00000262554.7	NP_006406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPTLC1	ENST00000262554.7	c.992C>T	p.Ser331Phe	missense_variant	Exon 11 of 15	1	NM_006415.4	ENSP00000262554.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, single submitter

Submissions by phenotype

Neuropathy, hereditary sensory and autonomic, type 1A Pathogenic:2

Jun 01, 2022

Solve-RD Consortium

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: provider interpretation

Variant confirmed as disease-causing by referring clinical team -

Apr 20, 2023

Duke University Health System Sequencing Clinic, Duke University Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Neuropathy, hereditary sensory and autonomic, type IA, severe Pathogenic:1

Oct 01, 2009

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.39
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.77	D
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D
M_CAP	Uncertain	0.25	D
MetaRNN	Pathogenic	0.92	D
MetaSVM	Uncertain	0.59	D
MutationAssessor	Uncertain	2.7	M
PhyloP100		9.7
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-4.5	D
REVEL	Pathogenic	0.83
Sift	Uncertain	0.022	D
Sift4G	Uncertain	0.024	D
Polyphen		0.22	B
Vest4		0.97
MutPred		0.76		Loss of glycosylation at S331 (P = 0.0686);
MVP		0.82
MPC		1.1
ClinPred		0.97	D
GERP RS		5.3
Varity_R		0.84
gMVP		0.98
Mutation Taster		=4/96	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs267607087; hg19: chr9-94809543;