chr19-18896057-G-A

Variant names:

• chr19-18896057-G-A
• rs1041161328
• NM_021267.5:c.16C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021267.5(CERS1):​c.16C>T​(p.Pro6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000012 in 836,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P6T) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000012 (0 hom.)
• Consequence: CERS1 NM_021267.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 0 publications found

Genes affected

CERS1 (HGNC:14253): (ceramide synthase 1) This gene encodes a ceramide synthase enzyme, which catalyzes the synthesis of ceramide, the hydrophobic moiety of sphingolipids. The encoded enzyme synthesizes 18-carbon (C18) ceramide in brain neurons. Elevated expression of this gene may be associated with increased longevity, while decreased expression of this gene may be associated with myoclonus epilepsy with dementia in human patients. This protein is transcribed from a monocistronic mRNA as well as a bicistronic mRNA, which also encodes growth differentiation factor 1. [provided by RefSeq, Jul 2016]

GDF1 (HGNC:4214): (growth differentiation factor 1) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. Studies in rodents suggest that this protein is involved in the establishment of left-right asymmetry in early embryogenesis and in neural development in later embryogenesis. The encoded protein is translated from a bicistronic mRNA that also encodes ceramide synthase 1. Mutations in this gene are associated with several congenital cardiovascular malformations. [provided by RefSeq, Jul 2016]

GDF1 Gene-Disease associations (from GenCC):

• right atrial isomerism

  Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics
• congenital heart defects, multiple types, 6

  Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Illumina, Ambry Genetics
• conotruncal heart malformations

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.04500076).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CERS1	NM_021267.5	c.16C>T	p.Pro6Ser	missense_variant	Exon 1 of 8	ENST00000623882.4	NP_067090.1
GDF1	NM_001492.6	c.-1307C>T		5_prime_UTR_variant	Exon 1 of 8	ENST00000247005.8	NP_001483.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CERS1	ENST00000623882.4	c.16C>T	p.Pro6Ser	missense_variant	Exon 1 of 8	1	NM_021267.5	ENSP00000485308.1
CERS1	ENST00000429504.6	c.16C>T	p.Pro6Ser	missense_variant	Exon 1 of 6	1		ENSP00000389044.1
GDF1	ENST00000247005.8	c.-1307C>T		5_prime_UTR_variant	Exon 1 of 8	1	NM_001492.6	ENSP00000247005.5
CERS1	ENST00000542296.6	c.-46+504C>T		intron_variant	Intron 1 of 5	1		ENSP00000437648.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000120 AC: 1 AN: 836198 Hom.: 0 Cov.: 23 AF XY: 0.00000259 AC XY: 1 AN XY: 386830

African (AFR) AF: 0.00 AC: 0 AN: 15798

American (AMR) AF: 0.00 AC: 0 AN: 1168

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5242

East Asian (EAS) AF: 0.00 AC: 0 AN: 3792

South Asian (SAS) AF: 0.00 AC: 0 AN: 17116

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 794

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1634

European-Non Finnish (NFE) AF: 0.00000131 AC: 1 AN: 763140

Other (OTH) AF: 0.00 AC: 0 AN: 27514

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.26
DANN	Benign	0.90
DEOGEN2	Benign	0.29	T;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.022	N
LIST_S2	Benign	0.27	T;T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.045	T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.76	N;N
PhyloP100		-1.5
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	-0.10	.;N
REVEL	Benign	0.010
Sift	Benign	0.92	.;T
Sift4G	Benign	0.77	T;T
Polyphen		0.0010	B;.
Vest4		0.033
MutPred		0.14		Gain of glycosylation at P6 (P = 0.0291);Gain of glycosylation at P6 (P = 0.0291);
MVP		0.030
ClinPred		0.050	T
GERP RS		-5.8
PromoterAI		-0.13	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.6
Varity_R		0.018
Mutation Taster		=96/4	polymorphism

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

Other links and lift over

dbSNP: rs1041161328; hg19: chr19-19006866;