6-149810956-A-T

Variant names:

• chr6-149810956-A-T
• rs7818
• NM_001360452.2:c.*378A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001360452.2(PCMT1):​c.*378A>T variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PCMT1 NM_001360452.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15
• Publications: 24 publications found

Genes affected

PCMT1 (HGNC:8728): (protein-L-isoaspartate (D-aspartate) O-methyltransferase) This gene encodes a member of the type II class of protein carboxyl methyltransferase enzymes. The encoded enzyme plays a role in protein repair by recognizing and converting D-aspartyl and L-isoaspartyl residues resulting from spontaneous deamidation back to the normal L-aspartyl form. The encoded protein may play a protective role in the pathogenesis of Alzheimer's disease, and single nucleotide polymorphisms in this gene have been associated with spina bifida and premature ovarian failure. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

ENSG00000285889 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCMT1	NM_001360452.2	c.*378A>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000464889.7	NP_001347381.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCMT1	ENST00000464889.7	c.*378A>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_001360452.2	ENSP00000420813.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 87644 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 45564

African (AFR) AF: 0.00 AC: 0 AN: 2692

American (AMR) AF: 0.00 AC: 0 AN: 2788

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3168

East Asian (EAS) AF: 0.00 AC: 0 AN: 5266

South Asian (SAS) AF: 0.00 AC: 0 AN: 5986

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4460

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 402

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 57080

Other (OTH) AF: 0.00 AC: 0 AN: 5802

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 20267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		3.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs7818; hg19: chr6-150132092;