1-78493354-T-A

Variant names:

• chr1-78493354-T-A
• NM_000959.4:c.611T>A

Variant summary

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

The NM_000959.4(PTGFR):​c.611T>A​(p.Leu204His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PTGFR NM_000959.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.93

Genes affected

PTGFR (HGNC:9600): (prostaglandin F receptor) The protein encoded by this gene is member of the G-protein coupled receptor family. This protein is a receptor for prostaglandin F2-alpha (PGF2-alpha), which is known to be a potent luteolytic agent, and may also be involved in modulating intraocular pressure and smooth muscle contraction in uterus. Knockout studies in mice suggest that the interaction of PGF2-alpha with this receptor may initiate parturition in ovarian luteal cells and thus induce luteolysis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGFR	NM_000959.4	c.611T>A	p.Leu204His	missense_variant	Exon 2 of 3	ENST00000370757.8	NP_000950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGFR	ENST00000370757.8	c.611T>A	p.Leu204His	missense_variant	Exon 2 of 3	1	NM_000959.4	ENSP00000359793.3
PTGFR	ENST00000370758.5	c.611T>A	p.Leu204His	missense_variant	Exon 3 of 4	1		ENSP00000359794.1
PTGFR	ENST00000370756.3	c.611T>A	p.Leu204His	missense_variant	Exon 2 of 4	1		ENSP00000359792.3
PTGFR	ENST00000497923.5	n.611T>A		non_coding_transcript_exon_variant	Exon 2 of 5	3		ENSP00000432599.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 24, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.611T>A (p.L204H) alteration is located in exon 2 (coding exon 1) of the PTGFR gene. This alteration results from a T to A substitution at nucleotide position 611, causing the leucine (L) at amino acid position 204 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.010
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.57	D;D;.
Eigen	Pathogenic	0.73
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.81	.;T;T
M_CAP	Benign	0.064	D
MetaRNN	Uncertain	0.74	D;D;D
MetaSVM	Uncertain	-0.065	T
MutationAssessor	Uncertain	2.4	M;M;M
PrimateAI	Uncertain	0.56	T
PROVEAN	Uncertain	-4.3	D;D;D
REVEL	Uncertain	0.61
Sift	Pathogenic	0.0	D;D;D
Sift4G	Uncertain	0.0020	D;D;D
Polyphen		0.99	D;D;D
Vest4		0.68
MutPred		0.57		Loss of stability (P = 0.0517);Loss of stability (P = 0.0517);Loss of stability (P = 0.0517);
MVP		0.65
MPC		0.88
ClinPred		1.0	D
GERP RS		5.8
Varity_R		0.69
gMVP		0.81

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: chr1-78959039;