rs1554851718

Variant names:

• chr10-89010783-T-G
• rs1554851718
• NM_000043.6:c.536T>G

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 12P and 1B. PM1 PM2 PP5_Very_Strong BP4

The NM_000043.6(FAS):​c.536T>G​(p.Leu179Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAS NM_000043.6 missense
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: -0.427
• Publications: 0 publications found

Genes affected

FAS (HGNC:11920): (Fas cell surface death receptor) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contains a death domain. It has been shown to play a central role in the physiological regulation of programmed cell death, and has been implicated in the pathogenesis of various malignancies and diseases of the immune system. The interaction of this receptor with its ligand allows the formation of a death-inducing signaling complex that includes Fas-associated death domain protein (FADD), caspase 8, and caspase 10. The autoproteolytic processing of the caspases in the complex triggers a downstream caspase cascade, and leads to apoptosis. This receptor has been also shown to activate NF-kappaB, MAPK3/ERK1, and MAPK8/JNK, and is found to be involved in transducing the proliferating signals in normal diploid fibroblast and T cells. Several alternatively spliced transcript variants have been described, some of which are candidates for nonsense-mediated mRNA decay (NMD). The isoforms lacking the transmembrane domain may negatively regulate the apoptosis mediated by the full length isoform. [provided by RefSeq, Mar 2011]

FAS Gene-Disease associations (from GenCC):

• autoimmune lymphoproliferative syndrome type 1

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• autoimmune lymphoproliferative syndrome

  Inheritance: AR, AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 7 uncertain in NM_000043.6
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 10-89010783-T-G is Pathogenic according to our data. Variant chr10-89010783-T-G is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 523313.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.1901528). . Strength limited to SUPPORTING due to the PP5.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000043.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAS	NM_000043.6	MANE Select	c.536T>G	p.Leu179Arg	missense	Exon 6 of 9	NP_000034.1	P25445-1
	FAS	NM_001410956.1		c.581T>G	p.Leu194Arg	missense	Exon 6 of 9	NP_001397885.1	A0A8Q3SIR6
	FAS	NM_152872.4		c.536T>G	p.Leu179Arg	missense	Exon 6 of 8	NP_690611.1	P25445-7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAS	ENST00000652046.1	MANE Select	c.536T>G	p.Leu179Arg	missense	Exon 6 of 9	ENSP00000498466.1	P25445-1
	FAS	ENST00000355279.2	TSL:1	c.536T>G	p.Leu179Arg	missense	Exon 6 of 8	ENSP00000347426.2	P25445-7
	FAS	ENST00000355740.8	TSL:1	c.536T>G	p.Leu179Arg	missense	Exon 6 of 8	ENSP00000347979.3	K9J972

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Likely pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
1	-	-	Autoimmune lymphoproliferative syndrome type 1 (1)
1	-	-	not provided (1)
1	-	-	Splenomegaly (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.57
BayesDel_addAF	Uncertain	0.057	T
BayesDel_noAF	Benign	-0.16
CADD	Benign	14
DANN	Benign	0.72
DEOGEN2	Uncertain	0.56	D
Eigen	Benign	-0.56
Eigen_PC	Benign	-0.85
FATHMM_MKL	Benign	0.033	N
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.048	D
MetaRNN	Benign	0.19	T
MetaSVM	Uncertain	-0.0039	T
MutationAssessor	Benign	1.7	L
PhyloP100		-0.43
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-2.1	N
REVEL	Uncertain	0.31
Sift	Benign	0.039	D
Sift4G	Uncertain	0.0090	D
Polyphen		0.94	P
Vest4		0.30
MutPred		0.54		Gain of MoRF binding (P = 0.0075)
MVP		0.46
MPC		1.0
ClinPred		0.57	D
GERP RS		0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.48
Mutation Taster		=76/24	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.19		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: rs1554851718; hg19: chr10-90770540;