rs755377592
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_019616.4(F7):c.1219G>A(p.Ala407Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,612,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
F7
NM_019616.4 missense
NM_019616.4 missense
Scores
7
9
3
Clinical Significance
Conservation
PhyloP100: 6.70
Genes affected
F7 (HGNC:3544): (coagulation factor VII) This gene encodes coagulation factor VII which is a vitamin K-dependent factor essential for hemostasis. This factor circulates in the blood in a zymogen form, and is converted to an active form by either factor IXa, factor Xa, factor XIIa, or thrombin by minor proteolysis. Upon activation of the factor VII, a heavy chain containing a catalytic domain and a light chain containing 2 EGF-like domains are generated, and two chains are held together by a disulfide bond. In the presence of factor III and calcium ions, the activated factor then further activates the coagulation cascade by converting factor IX to factor IXa and/or factor X to factor Xa. Defects in this gene can cause coagulopathy. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing to generate mature polypeptides. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PM1
In a disulfide_bond (size 28) in uniprot entity FA7_HUMAN there are 13 pathogenic changes around while only 0 benign (100%) in NM_019616.4
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.965
PP5
Variant 13-113118892-G-A is Pathogenic according to our data. Variant chr13-113118892-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 374352.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
F7 | NM_019616.4 | c.1219G>A | p.Ala407Thr | missense_variant | 8/8 | ENST00000346342.8 | NP_062562.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F7 | ENST00000346342.8 | c.1219G>A | p.Ala407Thr | missense_variant | 8/8 | 1 | NM_019616.4 | ENSP00000329546.4 | ||
F7 | ENST00000375581.3 | c.1285G>A | p.Ala429Thr | missense_variant | 9/9 | 1 | ENSP00000364731.3 | |||
F7 | ENST00000541084.5 | c.1033G>A | p.Ala345Thr | missense_variant | 6/6 | 2 | ENSP00000442051.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000765 AC: 19AN: 248338Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135056
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460138Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 726316
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Factor VII deficiency Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Baylor Genetics | Jun 30, 2014 | Our laboratory reported dual molecular diagnoses in F7 (NM_000131.4, c.1285G>A) and MECP2 (NM_004992.3, c.332G>A) in this individual with reported features of motor delay, intellectual disability, hypotonia, bilateral sensorineural hearing loss, skeletal abnormalities, hypertrichosis, and factor VII deficiency. The F7 variant has been previously found in patients with Factor VII deficiency (FA7D) [MIM:227500] (PMID 18976247), and is considered likely pathogenic. The patient's mother was similarly affected with factor VII deficiency and was homozygous for the variant. Heterozygotes are expected to be asymptomatic carriers. - |
F7-related disorder Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 26, 2023 | The F7 c.1285G>A variant is predicted to result in the amino acid substitution p.Ala429Thr. This variant (aka p.Ala369Thr) has been reported in individuals with Factor VII deficiency (Herrmann et al 2009. PubMed ID: 18976247; Ravanbod et al. 2022. PubMed ID: 36760778; Pshenichnikova et al. 2023. PubMed ID: 37761907). A different missense substitution at this same codon (c.1286C>T, Ala429Val) has been reported in an individual with factor VII deficiency (Tang et al. 2022. PubMed ID: 35349734) suggesting that substitution of amino acid residue Ala429 is not tolerated. This variant is reported in 0.041% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as likely pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
.;.;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
.;.;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;D;D
REVEL
Pathogenic
Sift
Uncertain
.;D;D
Sift4G
Uncertain
D;D;D
Polyphen
1.0
.;D;D
Vest4
MutPred
0.77
.;.;Gain of catalytic residue at T430 (P = 0);
MVP
MPC
0.73
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at