20-44622588-C-T

Position:

• chr20-44622588-C-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2_Supporting PM3_Strong PVS1_Strong PP4_Moderate

This summary comes from the ClinGen Evidence Repository: The c.845G>A (NM_000022.4) variant in ADA is a missense variant predicted to cause substitution of Arginine by Glutamine at amino acid 282 (p.Arg282Gln). This variant is considered in the PVS1 criteria based on experimental evidence indicating that it has the effect of affecting the splicing site. In line with the predictions of splicing algorithms, experimental validation (from Dr. Mike Hershfield - Internal Communication) has established that the variant occurs at the splice junction between exon 9 and intron 10 and has been shown to cause aberrant splicing in peripheral blood leukocytes (PBL) of a female Arab patient with ADA-SCID. Based on this, we classify PVS1 at a Strong level, as it results in the loss of more than 10% of the protein, and other pathogenic variants have already been described downstream (e.g., NM_000022.4(ADA):c.870C>A (p.Tyr290Ter), Pathogenic according to SCID VCEP specifications).The highest population minor allele frequency in gnomAD v4 is 0.000005310 (12/1180048 alleles) in European (non-Finnish) population, which is lower than the ClinGen SCID VCEP threshold (<0.0001742) for PM2_Supporting, meeting this criterion (PM2_Supporting). PMID:19830125: 14-month-old Arab boy: Family history of SCID 0.5pts + T-B-NK- profile 0.5pts + Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5pts + Reduced ADA enzyme activity 1pt, total=2.5 pts, PP4_Moderate. PMID:32307643, Patients 3 and 25, both are homozygous, reaching the maximum of 1 point for homozygous occurrence. From the same report, patient 2: Compound heterozygous,c.221G>T, p.G74V, Likely Pathogenic according to SCID VCEP specifications; 1 point. Total 2 points, PM3_Strong.In summary, this variant meets the criteria to be classified as Pathogenic for SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PVS1_Strong, PM2_Supporting, PP4_Moderate, and PM3_Strong. (VCEP specifications version 1.0). LINK:https://erepo.genome.network/evrepo/ui/classification/CA9871496/MONDO:0007064/114

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: ADA NM_000022.4 missense, splice_region
• Scores: Splicing: ADA: 0.9993
• Clinical Significance: Pathogenic reviewed by expert panel P:5 U:2
• Conservation: PhyloP100: 2.92

Genes affected

ADA (HGNC:186): (adenosine deaminase) This gene encodes an enzyme that catalyzes the hydrolysis of adenosine to inosine in the purine catabolic pathway. Various mutations have been described for this gene and have been linked to human diseases related to impaired immune function such as severe combined immunodeficiency disease (SCID) which is the result of a deficiency in the ADA enzyme. In ADA-deficient individuals there is a marked depletion of T, B, and NK lymphocytes, and consequently, a lack of both humoral and cellular immunity. Conversely, elevated levels of this enzyme are associated with congenital hemolytic anemia. [provided by RefSeq, Sep 2019]

PKIG (HGNC:9019): (cAMP-dependent protein kinase inhibitor gamma) This gene encodes a member of the protein kinase inhibitor family. Studies of a similar protein in mice suggest that this protein acts as a potent competitive cAMP-dependent protein kinase inhibitor, and is a predominant form of inhibitor in various tissues. The encoded protein may be involved in osteogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADA	NM_000022.4	c.845G>A	p.Arg282Gln	missense_variant, splice_region_variant	9/12	ENST00000372874.9
ADA	NM_001322051.2	c.773G>A	p.Arg258Gln	missense_variant, splice_region_variant	8/11
ADA	NM_001322050.2	c.440G>A	p.Arg147Gln	missense_variant, splice_region_variant	8/11
ADA	NR_136160.2	n.872+241G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADA	ENST00000372874.9	c.845G>A	p.Arg282Gln	missense_variant, splice_region_variant	9/12	1	NM_000022.4	P4

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152236 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251334 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135858

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000109 AC: 16 AN: 1461880 Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9 AN XY: 727246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000989

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152236 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74378

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5 Uncertain:2

Revision: reviewed by expert panel

Submissions by phenotype

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency Pathogenic:4 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 17, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Aug 24, 2017	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen	Jan 23, 2024	The c.845G>A (NM_000022.4) variant in ADA is a missense variant predicted to cause substitution of Arginine by Glutamine at amino acid 282 (p.Arg282Gln). This variant is considered in the PVS1 criteria based on experimental evidence indicating that it has the effect of affecting the splicing site. In line with the predictions of splicing algorithms, experimental validation (from Dr. Mike Hershfield - Internal Communication) has established that the variant occurs at the splice junction between exon 9 and intron 10 and has been shown to cause aberrant splicing in peripheral blood leukocytes (PBL) of a female Arab patient with ADA-SCID. Based on this, we classify PVS1 at a Strong level, as it results in the loss of more than 10% of the protein, and other pathogenic variants have already been described downstream (e.g., NM_000022.4(ADA):c.870C>A (p.Tyr290Ter), Pathogenic according to SCID VCEP specifications). The highest population minor allele frequency in gnomAD v4 is 0.000005310 (12/1180048 alleles) in European (non-Finnish) population, which is lower than the ClinGen SCID VCEP threshold (<0.0001742) for PM2_Supporting, meeting this criterion (PM2_Supporting). PMID: 19830125: 14-month-old Arab boy: Family history of SCID 0.5pts + T-B-NK- profile 0.5pts + Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5pts + Reduced ADA enzyme activity 1pt, total=2.5 pts, PP4_Moderate. PMID: 32307643, Patients 3 and 25, both are homozygous, reaching the maximum of 1 point for homozygous occurrence. From the same report, patient 2: Compound heterozygous,c.221G>T, p.G74V, Likely Pathogenic according to SCID VCEP specifications; 1 point. Total 2 points, PM3_Strong. In summary, this variant meets the criteria to be classified as Pathogenic for SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PVS1_Strong, PM2_Supporting, PP4_Moderate, and PM3_Strong. (VCEP specifications version 1.0). -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 26, 2024	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 282 of the ADA protein (p.Arg282Gln). This variant also falls at the last nucleotide of exon 9, which is part of the consensus splice site for this exon. This variant is present in population databases (rs751635016, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of adenosine deaminase deficiency (PMID: 19179314, 19830125, 27129325; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 402341). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 10, 2021	- -

Severe combined immunodeficiency disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Apr 19, 2018

Variant summary: ADA c.845G>A (p.Arg282Gln) results in a conservative amino acid change located in the Adenosine/AMP deaminase domain of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant is located in the last nucleotide of exon 9, suggesting it may interfere with proper splicing. 5/5 in silico prediction tools predict that the variant abolishes or weakens the 5' donor site. However, these predictions have yet to be tested in functional studies. The variant allele was found at a frequency of 7.2e-06 in 277232 control chromosomes (gnomAD and publications). This frequency is not higher than expected for a pathogenic variant in ADA causing Severe Combined Immunodeficiency Syndrome (7.2e-06 vs 0.0016), allowing no conclusion about variant significance. The variant, c.845G>A, has been reported in the literature in multiple individuals affected with Severe Combined Immunodeficiency Syndrome, both as a homozygous and compound heterozygous allele (Aiuti_2009, Hellani_2009, Sauer_2012). These data indicate that the variant is very likely to be associated with disease. One publication reports experimental evidence evaluating ADA activity in patient blood mononuclear cells, which showed <10% of normal activity compared to healthy controls (Aiuti_2009). A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as "uncertain significance," however, a disclaimer is included in the description stating that the variant has not undergone full assessment. Based on the evidence outlined above, the variant was classified as pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jun 02, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Reported in1 homozygous arab boy with severe combined immunodeficiency (Hellani-2009) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	33
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.79	D;D
Eigen	Benign	0.058
Eigen_PC	Benign	0.17
FATHMM_MKL	Benign	0.71	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Benign	0.049	D
MetaRNN	Uncertain	0.70	D;D
MetaSVM	Uncertain	0.022	D
MutationAssessor	Benign	0.80	N;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-1.7	N;N
REVEL	Uncertain	0.57
Sift	Benign	0.19	T;T
Sift4G	Benign	0.26	T;T
Polyphen		0.72	P;.
Vest4		0.44
MutPred		0.81		Gain of methylation at K284 (P = 0.1989);.;
MVP		0.99
MPC		0.20
ClinPred		0.64	D
GERP RS		5.1
Varity_R		0.49
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.63		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.63		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs751635016; hg19: chr20-43251229;