rs11555566

Variant names:

• chr20-44626579-T-A
• NM_000022.4:c.239A>T

Your query was ambiguous. Multiple possible variants found:

• chr20-44626579-T-A
• chr20-44626579-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_000022.4(ADA):​c.239A>T​(p.Lys80Ile) 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 pathogenic 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. K80R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ADA NM_000022.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.868

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADA	NM_000022.4	c.239A>T	p.Lys80Ile	missense_variant	Exon 4 of 12	ENST00000372874.9	NP_000013.2
ADA	NM_001322051.2	c.239A>T	p.Lys80Ile	missense_variant	Exon 4 of 11		NP_001308980.1
ADA	NM_001322050.2	c.-51A>T		5_prime_UTR_variant	Exon 4 of 11		NP_001308979.1
ADA	NR_136160.2	n.331A>T		non_coding_transcript_exon_variant	Exon 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADA	ENST00000372874.9	c.239A>T	p.Lys80Ile	missense_variant	Exon 4 of 12	1	NM_000022.4	ENSP00000361965.4
ADA	ENST00000695995.1	c.216+2470A>T		intron_variant	Intron 3 of 8			ENSP00000512318.1
ADA	ENST00000695991.1	c.216+2470A>T		intron_variant	Intron 3 of 7			ENSP00000512314.1
ADA	ENST00000696038.1	n.237A>T		non_coding_transcript_exon_variant	Exon 4 of 9			ENSP00000512344.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.55
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.11
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.94	D;D
Eigen	Benign	-0.063
Eigen_PC	Benign	-0.012
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.97	D;D
M_CAP	Pathogenic	0.32	D
MetaRNN	Pathogenic	0.87	D;D
MetaSVM	Uncertain	0.46	D
MutationAssessor	Uncertain	2.3	M;.
PrimateAI	Benign	0.43	T
PROVEAN	Pathogenic	-5.8	D;D
REVEL	Pathogenic	0.71
Sift	Uncertain	0.0050	D;D
Sift4G	Benign	0.073	T;T
Polyphen		0.11	B;.
Vest4		0.64
MutPred		0.70		Loss of methylation at K80 (P = 0.0143);Loss of methylation at K80 (P = 0.0143);
MVP		0.94
MPC		0.78
ClinPred		0.99	D
GERP RS		2.6
Varity_R		0.77
gMVP		0.76

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-43255220;