rs765287423

Variant names:

• chr11-59639325-T-C
• rs765287423
• NM_152716.3:c.2108A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-59639325-T-C
• chr11-59639325-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152716.3(PATL1):​c.2108A>G​(p.Asp703Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000214 in 1,399,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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: 0.0000021 (0 hom.)
• Consequence: PATL1 NM_152716.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.44

Genes affected

PATL1 (HGNC:26721): (PAT1 homolog 1, processing body mRNA decay factor) Enables poly(G) binding activity and poly(U) RNA binding activity. Involved in P-body assembly and deadenylation-dependent decapping of nuclear-transcribed mRNA. Located in P-body and cytosol. Colocalizes with CCR4-NOT complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255139 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14669299).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PATL1	NM_152716.3	c.2108A>G	p.Asp703Gly	missense_variant	Exon 17 of 19	ENST00000300146.10	NP_689929.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PATL1	ENST00000300146.10	c.2108A>G	p.Asp703Gly	missense_variant	Exon 17 of 19	1	NM_152716.3	ENSP00000300146.9
ENSG00000255139	ENST00000531108.1	n.223T>C		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000255139	ENST00000531311.1	n.65T>C		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000255139	ENST00000661394.1	n.582T>C		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000214 AC: 3 AN: 1399078 Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1 AN XY: 690092

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: 0.00000278

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.092	T
Eigen	Benign	-0.057
Eigen_PC	Benign	0.12
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.83	T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.6	L
PrimateAI	Benign	0.32	T
PROVEAN	Uncertain	-2.8	D
REVEL	Benign	0.093
Sift	Benign	0.080	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.23	B
Vest4		0.24
MutPred		0.33		Gain of glycosylation at S702 (P = 0.0242);
MVP		0.093
MPC		0.37
ClinPred		0.70	D
GERP RS		5.7
Varity_R		0.41
gMVP		0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs765287423; hg19: chr11-59406798;