NM_012305.4:c.1462G>C

Variant names:

• chr11-993293-G-C
• NM_012305.4:c.1462G>C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_012305.4(AP2A2):​c.1462G>C​(p.Ala488Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: AP2A2 NM_012305.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.01

Genes affected

AP2A2 (HGNC:562): (adaptor related protein complex 2 subunit alpha 2) The protein encoded by this gene is a subunit of the AP-2 adaptor protein complex, which is involved in linking lipid and protein membrane components with the clathrin lattice. This interaction supports the formation of clathrin-coated vesicles, and the encoded subunit aids in the process by binding polyphosphoinositide-containing lipids in the cell membrane. [provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.826

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP2A2	NM_012305.4	c.1462G>C	p.Ala488Pro	missense_variant	Exon 12 of 22	ENST00000448903.7	NP_036437.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP2A2	ENST00000448903.7	c.1462G>C	p.Ala488Pro	missense_variant	Exon 12 of 22	1	NM_012305.4	ENSP00000413234.3
AP2A2	ENST00000332231.9	c.1465G>C	p.Ala489Pro	missense_variant	Exon 12 of 22	1		ENSP00000327694.5
AP2A2	ENST00000528815.5	n.1465G>C		non_coding_transcript_exon_variant	Exon 12 of 21	2		ENSP00000431630.1
AP2A2	ENST00000687792.1	n.1462G>C		non_coding_transcript_exon_variant	Exon 12 of 21			ENSP00000508951.1
AP2A2	ENST00000687890.1	n.1462G>C		non_coding_transcript_exon_variant	Exon 12 of 21			ENSP00000510756.1
AP2A2	ENST00000693238.1	n.1462G>C		non_coding_transcript_exon_variant	Exon 12 of 20			ENSP00000510648.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.87e-7 AC: 1 AN: 1456058 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724572

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.01e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Benign	-0.090
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.37	.;T
Eigen	Uncertain	0.49
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Benign	0.044	D
MetaRNN	Pathogenic	0.83	D;D
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	1.7	.;L
PrimateAI	Pathogenic	0.86	D
PROVEAN	Uncertain	-3.0	D;D
REVEL	Uncertain	0.31
Sift	Benign	0.033	D;D
Sift4G	Benign	0.067	T;T
Polyphen		1.0	D;D
Vest4		0.67
MutPred		0.67		.;Gain of catalytic residue at A488 (P = 0.0576);
MVP		0.50
MPC		1.8
ClinPred		0.95	D
GERP RS		3.7
Varity_R		0.66
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: chr11-993293;